I now solved my wix v3 votive problems with newer builds of wix. The problem was that from a specific wix build on, the standard configuration was changed from any cpu to x86 and any cpu was not longer supported. I used my old .wixproj without change in newer version without discovering any problems.
When I changed to 3.0.4220.0, the TFS source control was not working any longer for the wix project itself but also causes the automatic checkout of items in other project types to not work.
After changing all any cpu references to x86 in my .wixproject everything worked fine.
It's really weird that this caused the TFS source control to not work correctly anymore.
Btw this is reproducable, so it's not just a hazard that it works now.