New build help - ALC889A & 7.1 - where is my subwoofer & why is everything backwards?

I've got a couple small issues with my new HTPC build that I hope someone can shed light on. Please note that through my backup SPDIF setting I am getting proper and full DD/DTS sound out of MKVs. I don't care that the sound is PCM 48khz, as long as it's the full 7.1 track and not matrixed. 48khz vs 96khz is really not all that bad to me, I just want my lossless PCM tracks, uncompressed: First the necessary specs:


Gigabyte GA-P35-DS4 Rev 2.1 motherboard w/Core 2 Duo

Onboard ALC889A (i.e. "the good onboard for BD")

NVidia GTS 250 1GB Video card

LG 8x BD Rom/DVDRW

Yamaha 6280B Amp


Software:

Vista x64, using MCE, desktop res set to 1080p24, guess MCE using the same?

Vista Codec Pack + Vista Codec Pack x64 addon, currently set to pass-through to SPDIF (see below)

Arcsoft TotalMediaTheater Platinum 3 (latest update - though should I consider PowerDVD 9?)

Latest Realtek HD Audio driver installed from realtek.com.tw


It is hooked up in the following manner:

DVI -> HDMI cable to the "DVR" hdmi in.

4 x miniplug-RCA adapters hooked into DVR in + 6xmultichannel analog in on the amp (i.e. 8 channels, though strangely all but the center/sub are hooked up the wrong way in order for the channels to be correct in the sound test!)

Coax SPDIF -> Amp as my currently-used backup sound method.




So here is my issue - I'm sure somebody has dealt with this before as I remember reading this exact issue here long ago when I was researching:


Strangely, I have to have all the RCAs aside from the center/sub channel backwards (red into white, white into red) in order for the Vista & Realtek sound test to be in the right order. My vista sound CP is set to 7.1, as is my MCE. I don't remember touching any settings in TMT, though I didn't see much to set. With that said, no matter which way I seem to set the RCAs on the sub/center input, or select "reverse sub/center", I can't seem to get my LFE working correctly. Sometimes I'd have ONLY a center channel on the center/sub sound tests, and other selections I'd hear my center tests through my subs and not anything in the centre. It seems to never be both, no matter the combination of RCA ordering and selecting "swap center/sub" in the Realtek control panel. Maybe I'm missing something, but what am I doing wrong?


As a related note, when I play a Blu Ray using MCE (i.e. the TMT plugin) or just the TMT plugin by itself, no matter whether I'm in my current SPDIF mode, or using the Multichannel analog, I only get 2 channels. No center, just 2 channels with only the "PLIIx" active on my amp, but all 7 channels showing when I'm in multichannel analog mode. Nothing comes out of my rear/side, centre, or subs. This may be a software setting or it may be related, but if anyone can help me it would be greatly appreciated.


As I side note, most of my MKVs seem to work but some refuse to play whether I enable or disable DXVA in the Vistacodecs plugin. Again likely a software issue that I can tinker with but if anyone knows why, feel free to add to it. Lastly, my desktop & MCE is jittery thanks to my 24hz video setting. Is there any way (aside from ReClock, which no longer works with TMT) to have my desktop locked at 60hz but my MCE at 24? Or even better, to have my MCE adapt to the video refresh rate as it starts playback? For instance, I have a lot of 30fps TV content on the PC and would love to have everything play smoothly, but would like to continue to have Blu Rays play at 24p (after all, my PLV-Z3000 has some nice 120hz frame conversion from 24p!) Thanks in advance!


Edit: figured out the center channel / subwoofer thing (slightly loose RCA lol). The rest still applies.