We've two different version control systems, currently using something even worse that SourceSafe. Where things got really bad was when we had to add functionality for the government that wasn't going to commercial customers. After several releases, we decided to go with one code base.

Heck, even Windows has one code base now. Server 2008 is built on Vista. Windows 7 is built on Server 2008.

>We use Vault and will move to Team System eventually. We have not had any problems that I am aware of with branching or merges.