You mention that your crossover is set to bypass, in which case I assume your crossover point is set in your receiver? Would go there to start fiddling with things.
But that aside, need to know a little more info. What speakers are you using? And where is your sub located in relation to your seating position and the speakers?
In my experience if the sub sounds excessively 'boomy' or cutting in and out like you say, there could be a number of factors at play.
Firstly, make sure the sub is not too loud. A lot of people tend to get a little heavy fisted with the volume control to try and get massive bass but all it does is destroy the cohesion of the sound.
Secondly, positioning. There is no simple rule here, and different people have different opinions. If your sub is in a corner, try moving it a little further out. Your sub appears to be front firing, is it firing directly at you or is there something in between your ears and the driver?
Thirdly, to go full circle, is the crossover. Depending on what speakers you have, make sure the crossover is not set too high otherwise the sub could be trying too hard. Conversly do not set it too low... even if you have large floorstanding speakers I would always cross them over at around the 60Hz - 80Hz mark (unless of course you have some monstrous Rockports or something....).
Aside from that, try some other test material as well. Don't just rely on one scene from one film. Try a couple of others, preferably films that you know very well. Also try some music. Personally I find it easier to hear how a sub is performing with music than film. It should be a smooth cohesive transition between the speakers and the sub. I.e. the sub should just be an extension of the main speakers, you shouldn't be able to detect that there is a sub even present. I'm not familiar with your M&K but going by the fact that it is sealed and has an 8" driver, it should be fast and tight, ideal for music.ÿ
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