I have a video file in MKV format
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.0
Format settings, CABAC : Yes
Format settings, ReFrames : 4 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 2h 49mn
Nominal bit rate : 1 068 Kbps
Width : 720 pixels
Height : 304 pixels
Display aspect ratio : 2.35:1
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.204
Writing library : x264 core 114 r1913 5fd3dce
Encoding settings : cabac=1 / ref=3 / deblock=1:0:0 / analyse=0x3:0x111 / me=hex / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=3 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=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=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=40 / rc=2pass / mbtree=1 / bitrate=1068 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00
Audio
ID : 2
Format : AAC
Format/Info : Advanced Audio Codec
Format profile : HE-AAC / LC
Codec ID : A_AAC
Duration : 2h 49mn
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 22.05 KHz / 11.025 KHz
Compression mode : Lossy

I tried to convert this to AVI (Xvid and AC3 5.1) but MeGUI is failing.
The process I conversion I usually follow are-
I use MKV extract to extract video and audio in raw format. Then I use MKV merge to convert .h264 to mkv by inputting the correct aspect ratio and codec used. Finally I use MeGUI to convert audio to AC3 5.1 (bit rate 448) and video to xvid and mux it to for avi. Most of the files I'm successful and i'm satisfied with MeGUI. With this particular file when I followed the usual routine but audio conversion failed. So I decreased the bit rate to 256 and all went fine until the final muxed file showing garbled audio and desync. Please suggest correct change. Thanking you