What I don't understand is how you can set the crossover setting on ONE amp to only affect one side. If you are coming in with a full range left and right to the amp and the setting on the amp is set for your subs, then by using the "Throught" 1/4 to the tops, you are actually sending full range to the tops. Full range will include bass which will in turn put more demands on that amplifier channel = high probability of early peaking if the speakers are being under powered.
You don't even have an Equalizer to control the side you want to control. Shortcuts to proper sound deployment will bring about problems like you are experiencing. For the kind of Gigs that you do my recommendation is that you get a two way crossover & EQ or a Driverrack plus two amps, one for tops and the other for subs. Put the damn thing in a rolling rack and ditch the friggin table.