It could also be one of the known issues with Windows XP and media files. (Specifially MPEG or AVI files).
If you have opened Windows Explorer to access files at anytime while your computer was running without a reboot it may explain the issue.
When you access a directly in Windows Explorer the operating systems reads each file and actually accesses information about the file. There is something strage about some MPEG & AVI files that causes Windows Explorer to keep attached to the files (and keep allocating memory/cpu). This can cause an inability to delete the file or a slowdown in other applications accessing similar files.
I have seen a patch on the Microsoft Knowledge Base for specific Divx files but you can search the net and see that the problem is wide spread.
Even if you close Windows Explorer you can still see "Explorer" in the task list with a strangely high memory count. Killing Explorer and rerunning it does not do the trick.
A reboot does.
However, if you DO NOT open Windows Explorer and just run TMPGEnc you will not see such a slow down on a 2nd encode.
(At least that has been my direct experience).
I actually use a 2nd computer to access files via my network to work around this issue on my encoding machine. The keeps the need to reboot down.
Hope this is helpful. (Like anything it may also be some completely other issue!!
)
Grantman