I've made a mistake with foams before I learned how to insert them correctly: It's not only about getting a seal. Depending on how much foam is in front of the InEar tubes's end, it can happen that you "stuff" too much of the foam into your ear canal when inserting the tips, with the result that there's only a tiny opening left for the sound to pass into your ear.
So yeah, when you hear less bass and more treble with foams, that doesn't necessarily mean you have a don't have a good seal, but you also could have inserted them not correctly or they simply don't fit (too big probably, because of too much foam before the tube begins).
That you describe the fit as uncomfortable as well, adds to my theory. When you have the right kind and size of foams for your ear, there is basically no way that they're uncomfortable and sound bad. For me, it was always too much hassle inserting them into my ears before I got a really good fit that I didn't have to correct every other song. Double flange silicone tips are the way to go IMO - same thing, though: You have to find the right kind, matching your ears and your InEars.