Protect LED's usually indicate clipping. i.e when the output power is too high, and may damage your speaker.
There is a term for the other way round, but it's been a long day at work and now my brain isn't functioning.
In any case, I think your amp is "monitoring" the signal/power going out the wire, and if there's too much resistance, it indicates that the speaker isn't handling it too well, so the amp cuts back. It could just be that the amp doesn't handle the way the sub is wired. i.e, if it's a 2ohm sub, the amp may find it too much resistance and cut out to protect itself.
If it's been running for a long time without any drama's, and it's just started to play up now, check the speaker wiring all the way to the sub itself, or make sure that you haven't flicked any bridging switches or something on the amp.
Hope that helps.