>>My 16F689 TMR1 counter is counting too well

After sleeping on your question, it sounds like you need a hardware debounce filter, possibly like

http://www.elexp.com/t_bounc.htm

I do not know how to add one in software when using the TMR1 as a counter. You could switch to another software means of counting all together (e.g., Interrupt on change of one of the port pins, etc) where adding software debounce would be a piece of cake.