OS X warns users the first time we open a newly downloaded application. The message is "xxx is an application downloaded from the internet. Are you sure you want to open it?"
It's a helpful warning. Problem is, for some apps I installed into Lion, it shows every time I open the app. Annoying.
I suspect the bug is that I installed them from my Admin account, but am using them from my non-admin everyday account. A permissions bug in other words. OS X usually has these, no reason for Lion to be different.
The fix for me has been to copy the app to my desktop. Then delete it from the Applications folder. Then drag it back to the desktop. This changed the permissions to read/write for me and ended the warnings. I then tested from my admin account and didn't get warnings there.
Not a bad workaround until Apple fixes this annoying bug.
Update: Thinking about this more, I bet the bug hits if you install from Admin, but never open the app from Admin. Next time I do this I'll switch to my Admin account and open it there.