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I have an application installed, and when I click on the shortcut to it from the start menu I am first prompted by the MSI installer and a UAC prompt. If the I allow the specified .msi file (C:\Windows\Installer\something.msi) to run, then the standard Windows installer window for the application shows up briefly with a progress bar and then my application runs. This happens every time.

If I just double-click the .exe that the shortcut points to in Program Files, then I don't see this. I've tried uninstalling and reinstalling several times. I have a feeling there is something broken in the windows installer database (if such a thing exists). Is there a tool or something that could help diagnose this issue?

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I think this will help you out. http://www.mydigitallife.info/windows-installer-cleanup-utility-free-download-to-fix-setup-installation-failure/

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I'm not even sure what expletive yer talking about and as for survival, you seem to be doing fine yourself even after said expletive. I'm a redneck, love to cuss and if I feel you stepped on my toes, I'll say it and then I probably won't remember your name. I'm not saying that your points aren't valid but I'll tell you honestly I don't really care. If someone negs w/out explanation they can expect a reply and more than likely one with a minor expletive like smartass or bonehead or dipshit. That's because it's common sense/courtesy to explain such things regardless of the survival odds :) – OG Chuck Low Dec 17 '11 at 6:25
LOL - I expect LOTS of downvotes :) Those that don't explain should expect profanity :) I'm bored, what can I say? :) As for understanding.. hell that's the only reason I BOTHER to bitch when someone negs with no comment. You ain't teaching nobody nuthin' like that :) – OG Chuck Low Dec 19 '11 at 14:29
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NOTE: While OG Chuck Low's answer is correct, the cleanup utility has been superseded by Windows 7's Install and Uninstall Fix It utility. The tool can be run directly from the linked page. I hope that helps!

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Nice call. I knew they had a "Fix It" utility but I was too lazy to look. I vote for your answer :) – OG Chuck Low Dec 15 '11 at 21:27
Thanks but this isn't resolving the issue. I can install and uninstall the app with no problems, it it just that the shortcut seems to want windows installer involved for some reason. – Josh Dec 16 '11 at 17:54
Just to make sure I get ya... you are saying you tried it and it didn't resolve your issue? Or you look and think "That won't work" so did not try it? If you tried it and it it's not working then I might suggest, since you noted double clicking the .EXE in the program directory didn't manifest the issue, just replace the target in your shortcut icon to the .EXE file. – OG Chuck Low Dec 16 '11 at 18:47
And if that don't work, just delete the desktop icon and then in the directory, make a shortcut off the .EXE file and then drop that on your desktop and see if that works properly. – OG Chuck Low Dec 16 '11 at 18:49
I tried the tool and it didn't fix it. I can create a separate shortcut and that works fine also. However, whenever I update the software (which is about once a week) I might have to deal with the weird shortcut issue again. This isn't a huge deal but I'm concerned that something is broken in Windows Installer that is causing this and might lead to bigger issues down the road. Also, the shortcut seems to be a special one because when I right-click it and go to properties, the target field is disabled. – Josh Dec 16 '11 at 19:24
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