Considering the power for the timer itself is drawn in parallel as it is plugged into the wall, the flicker issue is the most realistic. A simple screw in module that screws into the bulb socket would be the same. If however, you have one that is hardwired in place of the wall switch, the unit draws low current through the light bulb itself even in the "off" setting.
I do happen to have a similar timer as the one described, and I have used it on conventional T-12 lighting with no issues at all. Most likely both are using a Triac for the control device for simplicity and cheapness of circuit construction, I highly doubt any issues would arise from the timer aspect directly. or it's circuitry.
Which leaves the matter of the flickering as the most likely culprit. Without testing in actual conditions, conjecture is all that can be done. Set it up while you are at home to watch how it behaves is the best suggestion if you are wedded to CFL's in that fixture, or that that timer for that fixture.
As an alternate program idea, if your timer has a "random" setting, use that instead. It randomizes the actual turn on period using the time setting as an "approximate start point."