This issue is related to Windows 7 and prior and does not happen on all system configurations. To my knowledge it is not an issue on Windows 8.1. However, until another solution can be found you may want to try using the utility OpenWithAdd.exe. You can download it from: http://windowsxp.mvps.org/openwithadd.htm
are you talking about GMD native file association or files that it can import? I never had issue in 7 or in windows 8.0 with file association
for the import files, I just simply associated them with the "open with.." and point to the GMD exe and then all those files would simply open with GMD...