PREMIERE PRO SLOW & NO RT FOR SOME QUICKTIME MOV

My premiere pro is very slow when  loading a project of 45.5 GB source files. It takes about four  minutes to load this project of mpeg 2 HDV files which it captured from  my Canon XH A1. The files are located on an eSATA RAID 0 HDD partitioned to 2TB and 1TB respectively and is powered by  Mapower TB 32 Raid controller.
Secondly my Mercury  Playback Engine is not offering real time playback on some quicktime mov  files. The footage is really choppy when playing back in CS5. These  files have been generated and rendered in after effects using Animation as the  compression type @ 1440 x 1080 25fps. In addition to that I have some stock footage 1920 x 1080 24fps from Actionbacks which have an  alpha channel. These files are not playing back in real time, despite  having the EVGA GTX 285 2GB GPU. Please note that I get a yellow bar but  no RT at all and I can't even render them to get the smooth playback required. Anyone knows qhy is this happening?
The software is installed on C drive 250GB HDD which is about 70GB free.
I have got a  Matrox RT X2 card installed with the beta drivers which is also  exhibiting the same problem. But this problem is non Matrox project.
Is  there anything I can do to improve perfomance and realtime playback  here. I have invested a lot in my current system to the extend that I am  now very disapoointed with the current perfomance.
Thank you for your assistance.
System
PP CS5
HP XW6600
Vista biz 64
EVGA GTX 285 2GB
Dual Quad Xeon 5450 @ 3Ghz (Total 8 cores)
24 GB RAM
3TB ESATA RAID 0
Matrox RT X2

I'd throw back to harm's explanation.
back and forth from 32 - 64, loading up quicktime server etc...
All I know is, on windows MS AVI, on OSX Quicktime(as if you have a choice)....
correction; as if I have a choice.

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