That sounds like something I had a problem with. Check to make sure the clock signal is only going to clock inputs. So in other words, don't run a clock into a gate. Trying to be smart and run your clock into a debouncer in veribest will not work. I tried it and it yelled at me. If you absolutely need the clock to run into a gate, that problem can be solved. Of course, I could be wrong. The 'blah, blah, blah' part is important.