While this is not the season for air conditioning, fluorescents located near AC vents often will flicker when the cold air blows on them. Is your wall timer electronic? Digital display? That may be the problem.

"I have some track lighting on my ceiling and its wired into a wall timer switch."

Unless the time has mechanical contacts and not a solid state switch it is distorting the voltage waveform just like a dimmer.
It also leaks a small amount of current even in the off state.
This can cause compact florescent lights to slowly build up enough charge to try and light, then quickly shut down when the charge is used.
The lights appear to 'flash' on (actually the striking circuit trying to get the bulb running) but without enough current available they cannot stay on.
If the other lights are low voltage their power supplies may also be having problems with a distorted waveform.

You should never run compact florescent lights or any type of low voltage lighting on a dimmer or solid state switch that is not listed by the light manufacturer as suitable.

It can damage the power supplies and lead to overheating and even fires.