Audio issue streaming movies

I have had my WDTV Live Plus HD since Janurary, never had a problem until the other day. I’ve been encoding my Blu-ray library to my network to be able to stream it to any tv in the house and it was going great until about a month ago. The drive where I stored all my moves died on me. I’m now back up and running with a RAID setup and am re-encoding all my movies using the same process but now several of them are having audio issues. It’s either badly out of sync, or is staticy, or garbled, etc. Not all of them are this way but all of them play fine on my computer and I have used the same process to encode every one of them:

AnyDVD HD to rip the files

EAC3TO to demux it 

a GUI program called AsxGUI to encode to .mkv using x.264

I only include the AVC video track and the highest quality audio (usually DTS-HD, DTS-Master, or TrueHD) that is usually encoded into a FLAC file, and tell AsxGUI not to recompress the audio. This is the process I’ve been using for months and never had a problem until recently. The only thing is that the newest firmware update came along in the meantime while my drive was out of commission. I tried rolling back to older firmware but that didn’t work either.

I know for a fact that one movie I encoded this way before the HDD crash played great, then when I re-encoded it afterward it wouldn’t work. Any theories. I have been going back and re-encoding with lesser audio but would love to have the higher quality audio back…

I think there’s not much I can suggest you other than remuxing again :S