Check the wiring of your subs in the box. If the speaker wires are touching eachother then the sound will cut out. You said it worked fine for a couple months then stopped working so that makes me think the power/ground wiring is correct. If they are wired in a series and you have one loose speaker wire in the box it will screw up both speakers and make them cut in and out. More then likely the amp is bridged in a series to the speakers and your pushin around 250 to each.......
I would check the wiring inside the box. You said you had a smell? Your coils are getting too hot, too much of that and your gonna need new speakers soon, Turn the gain down. The gain on your amp needs to match the pre-out voltage on your headunit for safe operation. Fine tunning of the settings and this can be raised but it takes alot of experience and knowledge to fine tune the settings. Alot of people think the gain is a volume, it is not!! Its determining the signal voltage to the amp. Too much voltage = amp clipping. After the wiring has been checked in the box and its fine, i would turn your gain down just a smidge.