Software Center not seeing installed software

[Exomancer]

I am using Ubuntu 12.04.

Many time I have opened the Ubuntu Software Center and noticed that software long installed shows up as not installed. I have also noticed that some software to be downloaded have duplicate entries. I find this frustrating at times. Which do I download? I have used Synaptic when I had no clue. I know that it has nothing to do with updating the apt list. As I said, some of these programs have been installed for months and I get updates regularly and have manually updated the list from the terminal many times.

Can anyone explain this or put forth a solution.

Thanks.

[Cheesehead]

Examples of the problem would be helpful.

What do you have installed that does not show up as installed? How, exactly, did you install it?

What in Software Center shows up twice?