(Comparing with how I have the ATC setup on the 1100)
In my case, the tray is in place before the downward travel of Z even begins (when grabbing a tool). If your tray was arriving late due to improperly set solenoid valve, low air pressure, or other, I think you would see it as being quite obvious and I doubt that's the issue.
More likely tool/spindle alignment. Either the entire ATC (did you install it and go through the basic alignment techniques using a bar mounted in spindle, etc.)? or more probably the slop in the ATC tray. I fought with some crashes for a bit when we first got this machine. There are several threads on the 'zone about this issue - but in a nutshell the tool tray is bolted onto a shaft (driven by the stepper for the ATC) and it uses a small set screw to lock it in place. That set screw can loosen, or wear a bit and become more wobbly.
Maybe have a read through this thread to see if it helps:
http://www.cnczone.com/forums/tormac...machinist.html
WW