Replacing Assets Works, and Doesn't Work.

I'm using a Dell 720 PC, QuadCore processor, Windows XP with all current service packs and patches, 4GB RAM, and Premier Production Studio CS3 (with all patches).
I have a dual-boot system, with a "Clean" install (only the OS, Premier, TMPGEncXpress and Cineform NeoScene) on one disk, and a "Messy" install on another disk (all the above listed software, plus everything else under the sun, including anti-virus and anti-spyware software, email/ftp clients Nero 7 etc).
I have an HD (1440x1080, 30FPS) project which was originally created on the Messy system. It's about 8 minutes long and created with a Canon XH-A1. The project consists of a video file (created in Adobe Media Encoder from the original Premier Pro CS3 project), one menu, one sub-menu, and two audio tracks.
I booted to the Clean system and opened the project. I had done some work on the audio tracks, and rather than re-do the entire DVD and menus, I used Encore's "Replace Asset" feature and swapped the old audio track with the new one. No problem.
Then I wanted to replace the main video asset with another, slightly higher quality version. I used the "Replace Asset" feature, as above, to replace the old video (a 250 MB M2V file) with the new one (also an M2V file, just slightly larger).
It seems Encore replaces the video in a 2-step process. The progress bar zipped across to 100% on the first step, then rapidly went to 50% on the second step. From there, the time-to-completion indicator continued to increase, but the process never progressed past 50%. I looked at Windows' Task Manager, and my Quad Core processor was running at 25% overall and there was almost no disk activity. After 5 minutes, I cancelled the operation. Encore never recovered, and I had to kill it. I tried again, with the same results.
I tried the exact same steps on the Messy Windows installation, and had no trouble replacing the video asset (it took about 6 seconds), so "something" on the Clean system is screwed up. I'd actually expect the Clean system to be the more reliable of the two!
Do you think a reinstall of Encore is the only way to solve this? Has anyone else experienced this problem, and if so, what was the solution?
Thanks.

Are you using the same file name to replace the assets?
If so - try using a different name for each incremental version instead as the cache might be getting confused/corrupted due to (apparent) multiple instances of the same asset.
Failing that, what happens if you create new timelines instead of attempting to replace?

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