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So I have tried ripping my Sopranos Season 6 Part 1 discs to MKV, and it is successful. The problem I am running into is that certain players can't play the audio for some reason. I was also planning on using Handbrake to downconvert to a smaller size and quality, but it is unable to read them also. Examples of a few programs that CAN play them are Media Player Classic, and the player in Boxee. However, VLC will not play it and Windows Media Player will play it but with no sound. Anyone have any ideas on what is wrong? I grabbed the info from one of the files using MediaInfo:

General
Complete name : Z:\Video\TV\Sopranos\Season 6\06x01 - Members Only.mkv
Format : Matroska
File size : 8.42 GiB
Duration : 52mn 20s
Overall bit rate : 23.0 Mbps
Encoded date : UTC 2009-09-29 01:04:46
Writing application : MakeMKV v1.4.7 beta win(x86-release)
Writing library : libmakemkv v1.4.7 beta (0.7.7/0.8.1) win(x86-release)

Video
ID : 1
Format : VC-1
Format profile : AP@L3
Codec ID : WVC1
Codec ID/Hint : Microsoft
Duration : 52mn 16s
Bit rate : 18.0 Mbps
Width : 1 920 pixels
Height : 1 080 pixels
Display aspect ratio : 16:9
Frame rate : 23.976 fps
Resolution : 24 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.361
Stream size : 6.56 GiB (78%)

Audio
ID : 2
Format : PCM
Codec ID : FFFE
Codec ID/Info : Extensible
Duration : 52mn 20s
Bit rate mode : Constant
Bit rate : 4 608 Kbps
Channel(s) : 6 channels
Sampling rate : 48.0 KHz
Resolution : 16 bits
Stream size : 1.68 GiB (20%)
Title : 3/2+1
Language : English

Menu
00:00:00.000 : en:Chapter 00
00:01:43.103 : en:Chapter 01
00:10:26.042 : en:Chapter 02
00:21:57.232 : en:Chapter 03
00:30:12.435 : en:Chapter 04
00:43:17.219 : en:Chapter 05
00:47:02.277 : en:Chapter 06
00:50:39.661 : en:Chapter 07

Any help would be appreciated, I am pretty much at my wits end at this point.

Your disc has audio in LPCM (uncompressed) format. MakeMKV saves it as WAV extended LPCM format to preserve channel assignment. Some programs unfortunately do not process this format correctly - notably VLC and MKVmerge (mkvmerge will be fixed soon). Your options are either to wait when mkvtoolnix will be fixed and convert WAV to FLAC or I can teach you how to patch 2 bytes in file so it will be more compatible but channel assignment will be lost. Both options suck, which one do you chose?

Thanks for the info. Both options definitely suck at the moment, but I think I will wait for it to be fixed in mkvtoolnix. I will just have to deal with the massive amount of room they take up for the time being. I am just glad I know what the problem is now.