I recently changed my approach with ripping blurays and DVDs from using VidCoder to MeGUI. Everything is great, and I'm quite happy with the video quality of the rips... Problem is, that my "portable" versions won't work on my Windows Phone 7 anymore. Zune can read the files, and when I try to sync them to the phone, it insists on converting them to wmv files with vc1 and wma audio.

I originally suspected that it was a problem with my x264 settings, but after extensive testing, it would seem that x264 is not the problem at all. I've tried going down as low as Main@L1.3 and it still won't sync to my phone. I then decided to take a file which I knew was good, demux it with My mp4box GUI, and re-mux it again. Funny thing is that now it won't sync to the phone (without converting), even though it's the same video stream inside.

I've tried playing with My MP4Box GUI settings to no avail. What can I do to get it to work? VidCoder did all the muxing for me previously, so I never had to play with settings like this. I've also tried using FFMPEG and some other mp4 muxer which I forget the name of.

Here's a MediaInfo of the good file:

Code:
General
Format                                   : MPEG-4
Format profile                           : Base Media / Version 2
Codec ID                                 : mp42
File size                                : 485 MiB
Duration                                 : 1h 26mn
Overall bit rate mode                    : Variable
Overall bit rate                         : 781 Kbps
Encoded date                             : UTC 2012-03-28 22:39:10
Tagged date                              : UTC 2012-03-29 01:39:00
Writing application                      : HandBrake 4472svn 2012030401
Xtra                                     : WM/MediaClassPrimaryID

Video
ID                                       : 1
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L3.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 1h 26mn
Bit rate mode                            : Variable
Bit rate                                 : 648 Kbps
Width                                    : 800 pixels
Height                                   : 336 pixels
Display aspect ratio                     : 2.40:1
Frame rate mode                          : Variable
Frame rate                               : 23.976 fps
Minimum frame rate                       : 23.974 fps
Maximum frame rate                       : 23.981 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.101
Stream size                              : 403 MiB (83%)
Writing library                          : x264 core 120
Encoding settings                        : cabac=1 / ref=3 /  deblock=1:0:0 / analyse=0x1:0x111 / me=hex / subme=2 / psy=1 /  psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=0 /  8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=0 /  threads=3 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 /  bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 /  b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=2 /  keyint=240 / keyint_min=24 / scenecut=40 / intra_refresh=0 /  rc_lookahead=10 / rc=crf / mbtree=1 / crf=23.0 / qcomp=0.60 / qpmin=3 /  qpmax=69 / qpstep=4 / ip_ratio=1.40 / aq=1:1.00
Encoded date                             : UTC 2012-03-28 22:39:10
Tagged date                              : UTC 2012-03-29 01:39:00
Color primaries                          : BT.709-5, BT.1361, IEC 61966-2-4, SMPTE RP177
Transfer characteristics                 : BT.709-5, BT.1361
Matrix coefficients                      : BT.709-5, BT.1361, IEC 61966-2-4 709, SMPTE RP177

Audio
ID                                       : 2
Format                                   : AAC
Format/Info                              : Advanced Audio Codec
Format profile                           : LC
Codec ID                                 : 40
Duration                                 : 1h 26mn
Bit rate mode                            : Variable
Bit rate                                 : 128 Kbps
Maximum bit rate                         : 280 Kbps
Channel(s)                               : 2 channels
Channel positions                        : Front: L R
Sampling rate                            : 48.0 KHz
Compression mode                         : Lossy
Delay relative to video                  : -83ms
Stream size                              : 79.4 MiB (16%)
Encoded date                             : UTC 2012-03-28 22:39:10
Tagged date                              : UTC 2012-03-29 01:39:00
And here's the same video, but re-muxed, and won't work:

Code:
General
Format                                   : MPEG-4
Format profile                           : Base Media / Version 2
Codec ID                                 : mp42
File size                                : 404 MiB
Duration                                 : 1h 26mn
Overall bit rate                         : 650 Kbps
Encoded date                             : UTC 2012-05-08 16:31:55
Tagged date                              : UTC 2012-05-08 16:31:55
Writing application                      : My MP4Box GUI 0.5.6.0 <http://my-mp4box-gui.zymichost.com>

Video
ID                                       : 201
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L3.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 1h 26mn
Bit rate                                 : 648 Kbps
Maximum bit rate                         : 3 733 Kbps
Width                                    : 800 pixels
Height                                   : 336 pixels
Display aspect ratio                     : 2.40:1
Original display aspect ratio            : 2.40:1
Frame rate mode                          : Constant
Frame rate                               : 23.976 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.101
Stream size                              : 403 MiB (100%)
Writing library                          : x264 core 120
Encoding settings                        : cabac=1 / ref=3 /  deblock=1:0:0 / analyse=0x1:0x111 / me=hex / subme=2 / psy=1 /  psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=0 /  8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=0 /  threads=3 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 /  bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 /  b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=2 /  keyint=240 / keyint_min=24 / scenecut=40 / intra_refresh=0 /  rc_lookahead=10 / rc=crf / mbtree=1 / crf=23.0 / qcomp=0.60 / qpmin=3 /  qpmax=69 / qpstep=4 / ip_ratio=1.40 / aq=1:1.00
Encoded date                             : UTC 2012-05-08 16:31:55
Tagged date                              : UTC 2012-05-08 16:32:17
Color primaries                          : BT.709-5, BT.1361, IEC 61966-2-4, SMPTE RP177
Transfer characteristics                 : BT.709-5, BT.1361
Matrix coefficients                      : BT.709-5, BT.1361, IEC 61966-2-4 709, SMPTE RP177