You don't say whether this is a new install or one that's been in service and recently developed the "run-on" problem. Age, time in service, rod/handle interface,water conditions, chemical exposure, etc. can all play a role in the performance.
You can view some troubleshooting videos at http://howto.flushmate.com and view or download service manuals for your specific model at http://www.flushmate.com/DocumentLibrary/.
For best results, you may want to jot down the serial number of the Flushmate and call tech support (the toll-free number is on the serial number label) for additional information and assistance.
Hope this helps.