What am I doing wrong--Choppy audio?

I have a legally owned copy of Goodfellas on BluRay. I am using the Bluray as a testbed before I buy more. What I would like to do is make a backup of the Bluray, store it on my PC and then serve it to perhaps Popcorn Hour's NMT, assuming I can get this to work.

I have a dual boot iMac computer with Win 7 on one partition and Snow Leopard on the other. I use the Windows partition to try to make a backup. My goal is to back up to a 2TB HD (FAT32) and then serve movies from the other partition, Snow Leopard.

Every time I make a backup of the movie, the video plays okbut the audio is choppy. I test the playback through Cyberlink's PowerDVD.

Here is the process I use.

1) I have AnyDVD running in the background.
2) I start TSRemux
3) I specify the source file to 00000.m2ts on the bluray disc, which is the largest file
4) I specify the destination which is on the 2TB FAT32 HD
5) I pick the only video stream listed which is VC1
6) I pick the audio stream 0, which I believe is Dolby Digital 5.1
7) I choose M2TS as the output format

I have tried this process twice, once with the Bypass Audio alignment option checked and once with it not checked; the result is the same.
I click Remux and wait.

When it is done, I load the new m2ts into PowerDVD and play it. The video comes across ok initially but the audio is choppy. Also, if I move further into the stream both the audio is choppy and the video seems to stutter, kind of like it can't catch up.

My conundrum is that I don't want to spend $300 for something like Popcorn hour if this isn't going to work. I've always wanted a media server to store my backups, but if it's not going to work I might as well just pop my owned blurays into a bluray player.

Any help or instructions as to what I'm doing wrong, or how to get this to work would be greatly appreciated.

Thanks!

Thanks for all of your responses.

First off, Serra, what you say makes perfect sense. At this point, it's more of a "I want to get it to work" rather than is it feasible to backup my collection this way. For me, I bought a 2 TB drive for $120 which should hold roughly 70 movies. I plan to buy only the movies that I wish to view more than once, this might be around 200 or so, so 3 2TB drives in not cost prohibitive for me.

Also, last night I reformatted my HDD and reran TSRemux and had the same issue. Basically what happens is that Goodfellas starts out with great audio and video in sync for the credits and the opening of when they're in the car but once they get out of the car the audio and video becomes choppy. When I relocate the stream to farther in the movie the video is in slow motion and the audio is still choppy, again, like it's trying to catch up. This is frustrating to me. Like I said, it's more of a personal goal to get this working than a feasibility issue. The movie plays fine from the BD drive and I can't imaging that the HDD would be slower.

Tonight I will troubleshoot more to see if I can just play the original m2ts on my computer. I believe I was able to do this...play it from the BD drive with AnyDVE and without remux and it worked fine. I'd like to say it is something I'm doing wrong with TSRemux, but I have no idea what. There's not very many options, at least in the GUI, not sure if there's a CLI or not.

Wraslor, or anyone else...what is the benefit of using makemkv over TSRemux? Do you think this will solve the issue? I'd certainly give it a try. Is there any difference in quality...my assumption is that MKV is just another container so quality depends upon the formats in the container...but why would that possibly work over m2ts?

Thank you all.

Actually, this was very simple and I feel dumb for not figuring this out sooner. My HDD is plugged into the USB port on my G15 keyboard...I am out of USB ports even with a hub. Of course, the G15 only supports USB 1.0, ugh. I swapped it with another cable, the HDD now going through USB 2.0 and everything plays back find using Power DVD.

Thanks for all your help.