Is there a problem using cfl bulbs on certain switch timers? If so, what is the problem? I have noticed that some timers states to use on regular light bulbs(incandescent) only.

If so, what is the problem?

The problem is the effects of the interaction of the CFL electronics and the timer electronics when the two are placed in a circuit together. Solid state timer switch kills CFLs (http://www.fieldlines.com/story/2009/2/11/35352/2027) discusses the effects of timers of triac design. Some mechanical timers or solid state relay type timers (example: Swylite (http://www.swylite.com/)) are compatible with CFLs.

You need to use dimmable CFL's.