Comment 1 for bug 1635778

It looks to me like the version number of the package you're generating is "older" than the one in the repository and is therefore getting "upgraded".

Currently in the repository this is the version of vim: 2:7.4.1689-3ubuntu1.1

Notice the "2" in front of the version which is the epoch field. You should set that to "3" for your package to ensure that your package doesn't get overwritten. I don't know how you do that with checkinstall but I'm sure you can look it up.

This isn't a problem with elementary os.