It might help if you describe the sequence of events that leads to the flooding.
In my experience, my skimmer used to give me trouble as follows:
1) Water is pumped into the skimmer, flows through the skimmer, then back into the tank. (obviously...)
2) On occasion, the outflow of the skimmer would slow and then air lock. Water would continue to pump INTO the skimmer caused the skimmer to essentially blow it's top...or dump water into the overflow cup and out the drain line.
There are other situations that could be causing your problem, but that is what happened to me in any case.
My solution BTW
, was to ensure that the outflow line remained clean at all times and to jiggle it now and then to ensure that any bubbles forming were spit out.