"Bigger difference"? The Project Phono Box MM does two jobs. It balances (equalises) the audio signal, and then it boosts the level.
The sound needs to be equalised because of the way vinyl works. When mastering for a vinyl pressing, the bass content has to be reduced dramatically. This is so that the stylus doesn't jump out of the groove on the bass beats.
The boost is needed because the signal level generated by a cartridge is tiny compared to a line level source such as a CD player. Without the pre-amp's boost, your Pioneer would be on full volume to hear maybe 1/10th of that you'd get with a normal source at -40dB. After the pre-amp has done its work, the signal will drive a line level input okay, though it will still be quieter than your other sources.
The Project Phono pre-amp is decent. It does the job without polluting the sound. I'm not sure what you mean by bigger difference. What extra magic do you think it should be doing?
I can think of a couple of things that would cause some distortion to the sound, but they would be symptoms of an incorrectly fitted/adjusted cartridge, or running the signal in to the wrong sort of input on the amp, or having a different phono pre-amp than the one you mentioned. All of them would affect nearly every record you play though, and you said some sound good, so I don't think from what you've written, and from knowing the gear you have, that they're likely causes.
Have you kept the stylus clean? Has the cantilever been damaged in some way? Are these used LPs you're playing, and have you heard them played on another system?
I think we've got to the point here where you need to go back and visit your dealer. The first stage is to have a chat with them and arrange to take your pre-amp box (+PSU) along with a couple of the LPs that exhibit this dull and underwater effect. Take a good one along too for comparison. A 3rd party opinion will help to get some perspective on the issues.