Does this problem happen on all application installations, or just certain ones? If it's just a few, I would just re-enable UAC during installation. Overall, I wouldn't recommend disabling UAC unless you have a good reason for doing so.
I've done some googling and it looks like this is a known issue for many applications when UAC is disabled. For example, this one from Adobe:
http://kb2.adobe.com/cps/333/333643.html
Quote:
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This utility extracts the contents to the user temporary folder [....] with User Account Control disabled, does not allow write and execute access to the %TEMP% folder.
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Hope that helps