Amplifier and Low Pass filter not responding after few minutes of correct output?
I guess some capacitor charges slowly and some part of your circuit drifts finally to the max or min voltage which the power supplies allow. You should find where the drift happens - check Vdd stability and separate the stages (=disconnect the left ends of interconnecting resistors and connect them to Vdd). 

There's missing or too high resistance DC path somewhere. Or an electrolytic capacitor is used with wrong polarity.

Also your opamp IC can be faulty and gets gradually hot somewhere in the chip.