Currently I'm using Source Safe with a legacy VB6 application and I've noticed countless times where the application is not updating the files correctly using the get latest version, or adding new files to a project. I just figure someone has to have a better way of using version control with VB6 applications.
Use something else - anything else. The three more popular free/open source solutions are git, mercurial, and svn. I doubt that git and mercurial integrate into VB6 but SVN does have an integration solution - you can find it here: http://svnvb6.tigris.org/
For what it's worth, I have gotten used to not having source code control integrated into my IDE, so integration wouldn't even be a factor in my decision if I were choosing a new solution.