GMgen does not display tools in 5.17.12. No behavior as in 5.16.4. Also occures with Ubuntu 11.10 (will post in separate issue.
Also occurs in Ubuntu. The issue appears to be related to preferences.
There was a bug in preferences that was forcing the GMGen plugins to be shown in pcgen, which it was not able to do. This preference has ben fixed. Once you have the fix, you may need to open preferences and close it again to reset the defaults to GMGen.