Try start>properties>start menu tab>customize>advanced tab>is the "list my recently opened documents" checked?
Regarding "windows user Assist MRU's" is a feature some programs have and if enabled will delete.If you have a prgram with this feature it might be configured to delete MRUs.
ccleaner has this feature,check this SCREEN SHOT and notice "other explorer MRUs"
Tom
For some reason my start menu no longer shows Recently Used Programs or Recently Used Documents. All other MRU lists seem to be working properly, just these two are blank. I tried clearing or setting it to display 0 programs, then restarting and setting it back to 6 but it still doesn't show. Any ideas appreciated.

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