There are no known issues with the 64-bit compiler. You will always get that error when you have extenders installed on your system that are newer than the version of the compiler you are using. Your do not need to select an extender into a compilation to get the error. Did you allow setup to install 64-bit WinBatch+Compiler as well as the 32-bit version? Have you entered new licensing information for the 64-bit compiler?
If the answer is yes to both of these question, the best thing to do is to perform a complete uninstall/reinstall of WinBatch.