When resetting the modules with the database cleaner this tool will clear out the modules table and rebuild the tree from the files. In this process the first new ID will be the next in line due to auto increment. However a bug in phpBB makes it that the "force re-check" link on the ACP main page will link to module ID 1 rather than the module name.
Hence this link will be broken afterwards. This issue will be resolved in phpBB 3.0.10 but the STK will need to receive a work around to remain backward compatible.

For referance: http://www.phpbb.com/customise/db/official_tool/stk/support/re_check_version_causes_general_error-t_93163