A family of Microsoft word processing software products for creating web, email, and print documents.
OK, so after too much searching I found there is no solution for the problem, at least no till MathType 6.7. Apparently even if you modify the registry, which I did, every time you start Word the problem appears again. This is because MathType runs a set of macros that conflict with Word's functionality for smart paste. See the MathType technical note about the issue here
The only solution they propose is that you deactivate the automatic start of MathType TB with Word start up, or that you deactivate MathType TB while using word, see this technical note , in any case you have to be fully aware that the problem does exist.
Hope this save some time to more people running into the same problem :)