I mainly use Eclipse (Java, C, Python & Perl). I've never run into the kind of issues VC presents, regardless of the language category. Most issues related to source control have been due to the limitations of the SCM tool used. That said, Git integration does suffer from idiosyncrasies on the part of the eGit plugin developers.

VC++ does do "magic" things when it comes to include files, resulting in code that may not work on another compiler.