Some electronic timers use the filament in the bulb to keep time. These timers are designed to replace a regular wall switch. They are usually not a plug in timers. They simply have 2 black wires. In order for the timer to keep time it needs to have a constant flow of electric. This is achieved by electrical current running through the filament of the bulb at a very low rate. Since CFL's do not have a filament, current will not pass through making it impossible for the timer to keep time.
Mechanical timers "like the plug in type", electronic timers with battery or timers with a neutral connection do not require a filament to keep time. Therefore you can use a cfl bulb. The directions just choose not to explain the difference. It's easier for them to just tell the public not to use them with a timer then to have to answer a rush of possible complaints from customers.
*Googled it and the above was on another forum*