I had this issue the other day and wanted to write it down both as a reminder to myself and a hint for anyone that might be suffering from it.
Basically, some programs (I had it with Broderbund Print Shop which seems to be the most commonly found option) that burn things to disc mess with settings that hose the pagefile, making the computer running badly and having the window to change it popup after every boot.
The fix is actually very easy and quite painless. Just drop to a command prompt and type:
sc config afs start= disabled
Reboot the computer and that should solve the issue, it did for me.