Problem exporting from large sequences

I'm reposting here becase it could be hardware related (the system is new), and because it wasn't answered on the CS5 forum and quickly got buried beneath 100 other threads. There's usually more in-depth support on this forum. Here goes:
I'm running CS5 5.02 on Windows 7 Professional 64-bit with an X58A-UD3R mobo, i7 930, 12 GB RAM, and a GTX 470. The footage is 4:3 NTSC DV, 29.97fps, 720x480. The sequence is DV NTSC Standard 48 kHz. OS on C drive, media and project on E drive, exporting to F drive.
I often put 100 clips or sometimes even 1000 clips on a sequence.
When I go to File-->Export and start exporting video for a small work area (10 seconds or less), it brings up a dialogue box that says "Encoding Sequence 01" and doesn't make any progress for a painfully long time if there are many clips on the sequence. The more clips in the sequence, the longer it waits before exporting. If I isolate the same clip in another empty sequence and try to export the same small work area, it quickly exports the file. As I add and delete clips from a sequence, the problem waxes and wanes. When there's over 200-300 clips, I've never seen it export the video because it just sits there forever "encoding".
I've tried this with several export formats: mpeg2, h264, quicktime, etc., with the same results. Exporting a still JPEG will quickly work on the large sequence, but it is very slow to export video.
It's as if Premiere is trying to encode the entire sequence first even though I've told it to only encode the small work area. It still only exports the small work area I requested, not the entire sequence.
Can someone please try to replicate this a few hundred clips and/or give me advice?

Thanks for your replies, guys.
I'm under deadline but will try running PPBM5 on Tuesday and post back here to see if you have ideas.
There must be something wrong with my setup, because although the project runs smoothly, the exporting lags significantly even with 100 or 200 clips. Surely CS5 should be able to export quickly from sequences as small as that. I had no problem doing this with previous versions of Premiere Pro.
Can anyone try throwing 100-200 clips onto a sequence to see if it causes any lag before exporting a small work area?

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