Lighting control devices....timers, photocells, and motion sensors.....can be problematic with fluorescent. Especially electronic devices like your timer.
Here is the reason......
Simple electronic in-line devices like maybe your timer are designed to replace a simple on/off switch in a box where only the HOT wire is present, not a ground or neutral. Therefore, they way they work is to "steal" a tiny amount of current. That is when the timer or photocell wants the lights to be OFF it is still passing just a few milliamps of current to operate its circuits, and be ready to switch when the time arrives. For incandescent bulbs, this current just passes through the bulb, and is so small that it does not even cause a little glow. But, flourescent bulbs DO NOT LIKE this set-up. It will cause the flickering etc. that you are seeing.
The only solution is to get a timer which is specifically rated for fluorescent. They are much more expensive, and often require a neutral and/ or a ground to be present in the switch box, and you may or may not have that.
Also, you have to look specifically at what kind of lamps/ballasts you have. Some of the timer/photo/motion devices will be rated for MAGNETIC ballast only, some for ELECTRONIC only, and some for BOTH. For a look at some devices and specs, try
www.wattstopper.com