Depends on where your "high swr" reading is.
If you are using a radio, two amps, and an antenna, the radio thinks the first amp is the antenna when that amp is switched on.
If your high SWR is between the radio and the first amp WHEN ITS TURNED ON, the problem is the input section of the first amp. When this amp is off, it sees either the second amp or the antenna, depending if the second amp is on.
If you are running a single 2 driving 4, then you have only one amp to deal with, but the same rules apply.
You should ALWAYS have your radio and amp set up together and then tune the antenna accordingly.
So, where ARE you taking your SWR reading at in the chain?