sorry guys but it's impossible to say if the batteries are at fault without having internal resistance numbers.
you're familiar but it goes like this, the batteries are warm but are they puffing? the flights are shorter, are they warming up when they're being charged? the batteries are puffing, are you running them at or beyond their limit (exceeding rated discharge amps)? there are symptoms but they all point to either ratings being exceeded (it looks like you're good there Shawn) or the batteries having higher than normal internal resistances.
when the packs develop resistance inside the cells the electricity flowing through them will cause heat to be created, just like a lightbulb. when you're charging, the resistance will generate heat just like when discharging. so if resistance has formed inside the packs, they will warm when being used, they'll warm when being charged, they won't take as much of a charge, and they won't last as long when you're flying them. lightbulbs get hot, you want your packs to be more like batteries and less like lightbulbs.
Shawn, it's possible the heat is ok....if flight times stay the same, if the packs don't puff, if they don't keep getting warmer and warmer as they are charged/discharged then the heat is probably an acceptable condition.
Gary, are you using the battery monitors from HobbyKing with the digital readout or just the alarms? the digital readouts will tell you the voltage of each cell and yes, one bad cell will cause those monitors to chirp.