the strange thing is it is the non amped speakers that are squeeling not the amped sub
if the sub is low passed then it may be squealing but you might not be hearing it. It is a good sign in a way, means your filters are doing their job

A way to test this would be...
Hopefully you are running full range preouts to your sub amp or can change them to full range without taking your HU out otherwise this won't work. Oh and it can't be a class D mono either but it should work on any 2/4ch.
turn the filters off on the amp or HU (or as above if you can really be bothered take the HU out and switch the RCA cables at the back of the HU from the 'sub' outputs to the 'front' outputs) then connect up any full range speaker, even a house one, to the amp but leave it at a low level. You will then be using the amp as a 'normal' amp rather than a bass amp. If you can hear the noise now then the amp is doing it but you just can't hear it through your sub
