ragezonegear,
think of the alpha areas as zeros and the effect you are applying as ones or, think of the alpha as a nothing and the effect as a something. nothing plus something is something. if you add zero to one you get one. the only way to keep from applying the ones to the zeros is to mask the zeros or make selections of the ones or zeros. FF doesnt do this. you have to do this in your graphic editor and then apply your filter to the area you want.
if you want to play with the alpha channel in FF use the 'set alpha' and 'get alpha' components within the editor, otherwise it's pretty much ignored. remember, just because the alpha is transparent doesnt mean it's not there or that something cant show in the other channels.
in a 24 bit image you have 3 channels, each is 8 bit adding up to the 24. when you add a fourth channel this is the alpha. it is also 8 bit, now adding your 24 up to 32. so, just because the alpha is blank doesnt mean the rest is.
If wishes were horses... there'd be a whole lot of horse crap to clean up!
Craig