OP
the box is in a the trunk of a car, box is sealed and im geussing about 2.5 cubic ftTurning the gain up all the way can send a clipped signal to the subwoofer, which, to put it simply, will blow your speaker.
Now, I have a couple guesses:
a) Your subwoofer is wired wrong. This could mean that the amplifier is seeing a higher impedance, which would mean less power to the subs.
b) Your sub is out of phase; this is related to a wiring problem, but it just means that your + and - wires are backwards. Take a 9V battery, touch your + and - wires that are going into your amplifer to the battery. (MAKE SURE THE WIRES ARE DISCONNECTED FROM YOUR AMP). If the sub pops out, your sub is in-phase, which is good.
c) Headunit may have a funky setting. Go through your owner's manual and make sure you don't have any settings wrong. Also check the filter on your amp/headunit, and make sure it's not set too high.
d) Shitty box or box placement. Your box has just about the largest effect on output. What sort of vehicle, what is the box placement in the vehicle, and what is the orientation of the sub on the box. Is the box ported or sealed? Do you know how it's internal airspace, or its outer dimensions?
When you say "before it was never this bad", are you saying that with this same setup it used to be good and all of a sudden went bad?
Check the voice coil on your sub to make sure the sub isn't blown. This would be my primary guess. It's rare to screw up your amp and have it only put out a fraction of power. It is usually all or none, rarely in between.