When the proxys are being built blender creates temporary that have the word "part" in their name (timecode and avi files). These files are erased once blender finishes building the proxys the first time, but if you rebuild the proxys then these files do not get deleted and the original files are not updated. (Checked the time the file was modified to confirm this.)
(PS. Build quality still has no effect. last report)
This only seems to only be a problem on windows.
Tested on Blender 2.62 official release (32bit and 64bit).
Windows 7 64bit and Ubuntu 11.04 32 bit (No problem here :)).
4GB ram
NVIDIA Quadro 1600M
T9500 Core 2 Duo @ 2.6 GHz.
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Works better but it still cant replace the proxy file if it is currently being used for the preview.
For example build the proxys. Then change the "Proxy render size" option from "Scene render size" to "Proxy size 25%". Then rebuild the proxys. The proxy file that is being used for the preview will not be replaced.