I finally got mkv conversion to work. It was no problem converting blu-rays to mkv, but megui kept throwing errors at me as I intended to lower the bit depth of the movie.
I've managed to get it right (don't ask why I don't know what the problem actually was). Problem is, when I'm opening it with any player without built in codecs it keeps loading for approximately half a minute. I don't have to wait that long when opening the MKV-File with the original bit depth. I know from other MKV movies this just can't be right. Therefore I'm asking what I've done wrong. First thought of mine was that I've chosen "ABR" in the x264 configuration popup of MeGui whereas I always read of 2 pass conversions.

Additionally I've mkvinfo outputs of both files with which maybe helped with.

Large File without bit depth compression:
(MKVInfo) + EBML head at 0
(MKVInfo) |+ EBML version: 1 at 5
(MKVInfo) |+ EBML read version: 1 at 9
(MKVInfo) |+ EBML maximum ID length: 4 at 13
(MKVInfo) |+ (Unknown element: EBMLMaxSizeLength; ID: 0x42f3 size: 4) at 17
(MKVInfo) |+ Doc type: matroska at 21
(MKVInfo) |+ Doc type version: 1 at 32
(MKVInfo) |+ Doc type read version: 1 at 36
(MKVInfo) + Segment, size 22112255565 at 40
(MKVInfo) |+ Seek head at 51
(MKVInfo) | + Seek entry at 62
(MKVInfo) | + Seek ID: 0x15 0x49 0xa9 0x66 (KaxInfo) at 65
(MKVInfo) | + Seek position: 72 at 72
(MKVInfo) | + Seek entry at 76
(MKVInfo) | + Seek ID: 0x16 0x54 0xae 0x6b (KaxTracks) at 79
(MKVInfo) | + Seek position: 179 at 86
(MKVInfo) | + Seek entry at 90
(MKVInfo) | + Seek ID: 0x1c 0x53 0xbb 0x6b (KaxCues) at 93
(MKVInfo) | + Seek position: 22112179157 at 100
(MKVInfo) |+ EbmlVoid (size: 3) at 108
(MKVInfo) |+ Segment information at 113
(MKVInfo) | + Muxing application: Haali DirectShow Matroska Muxer 1.9.42.1 at 124
(MKVInfo) | + Writing application: eac3to at 167
(MKVInfo) | + Segment UID: 0xdc 0x08 0x48 0x18 0x33 0xaf 0x22 0x40 0x92 0x3a 0x19 0x0c 0x80 0x97 0xd5 0x8f at 176
(MKVInfo) | + Date: Sun Mar 01 22:39:11 2009 UTC at 195
(MKVInfo) | + Timecode scale: 1000000 at 206
(MKVInfo) | + Duration: 6520.639s (01:48:40.639) at 213
(MKVInfo) |+ Segment tracks at 220
(MKVInfo) | + A track at 233
(MKVInfo) | + Track number: 1 at 237
(MKVInfo) | + Track UID: 1 at 240
(MKVInfo) | + Track type: video at 244
(MKVInfo) | + Lacing flag: 0 at 247
(MKVInfo) | + Default flag: 0 at 250
(MKVInfo) | + Codec ID: V_MPEG2 at 253
(MKVInfo) | + CodecPrivate, length 150 at 262
(MKVInfo) | + Default duration: 41.708ms (23.976 fps for a video track) at 416
(MKVInfo) | + Video track at 424
(MKVInfo) | + Pixel width: 1920 at 426
(MKVInfo) | + Pixel height: 1080 at 430
(MKVInfo) | + Display width: 1920 at 434
(MKVInfo) | + Display height: 1080 at 439
(MKVInfo) | + Language: und at 444
(MKVInfo) |+ Cluster at 451
Small File with bit depth set to 10 MBit/s
(MKVInfo) + EBML head at 0
(MKVInfo) |+ EBML version: 1 at 5
(MKVInfo) |+ EBML read version: 1 at 9
(MKVInfo) |+ EBML maximum ID length: 4 at 13
(MKVInfo) |+ (Unknown element: EBMLMaxSizeLength; ID: 0x42f3 size: 4) at 17
(MKVInfo) |+ Doc type: matroska at 21
(MKVInfo) |+ Doc type version: 1 at 32
(MKVInfo) |+ Doc type read version: 1 at 36
(MKVInfo) + Segment, size unknown at 40
(MKVInfo) |+ Segment information at 45
(MKVInfo) | + Muxing application: Haali Matroska Writer b0 at 50
(MKVInfo) | + Writing application: x264 at 77
(MKVInfo) | + Timecode scale: 50000 at 84
(MKVInfo) | + Duration: 0.000s (00:00:00.000) at 90
(MKVInfo) |+ Segment tracks at 97
(MKVInfo) | + A track at 102
(MKVInfo) | + Track number: 1 at 104
(MKVInfo) | + Track UID: 1 at 107
(MKVInfo) | + Track type: video at 111
(MKVInfo) | + Lacing flag: 0 at 114
(MKVInfo) | + Codec ID: V_MPEG4/ISO/AVC at 117
(MKVInfo) | + CodecPrivate, length 39 at 134
(MKVInfo) | + Default duration: 41.708ms (23.976 fps for a video track) at 176
(MKVInfo) | + Video track at 184
(MKVInfo) | + Pixel width: 1920 at 186
(MKVInfo) | + Pixel height: 1080 at 190
(MKVInfo) | + Display width: 16 at 194
(MKVInfo) | + Display height: 9 at 198
(MKVInfo) |+ Cluster at 202
Thanks for paying attention. Any help will be appreciated.