I have an alpine head unit and the Imprint audessy box but have not installed the imprint unit yet. Lotta help I am.
My first thought would be check your speakers for damage- one could be starting to let go and distorting just enough...

I't's been my experience that a decent mp3 is not nearly as foul as an overcompressed (modern) cd, so I wouldn't blame the source or lack of audessy right off. With the noise in a car you naturally turn up the vol and increase the potential for clipping/distortion. What kind of car/system do you have? I've heard that a decent oem deck is equivelent in sq to a mid-line aftermarket,so that may or may not gain you anything. A modest amp may be all you need.
Having said that- alpine sells a stand alone imprint solution, but thats not cheap.