Here are a couple things to try.
1. Bypass the clarion eq and plug the mp3 player directly into the amp.
2. If you have a laptop hook it to the system and see if it works better, both direct and through the Clarion.
3. If the unit is like my Creative Nomad, the headphone outputs are a better source then their line outs, should be the other way around but the headphone out was consistently better in different setups, so I just gave up on the line outs. Set all your tone controls on the MP3 player to flat, no bass boost, no increased output.
When testing some speakers recently I discovered the my laptop audio output sounded way better then my mp3 player. Your MP3 Player may not see the load it is expecting so it may be acting funny. You may need to turn it way down or way up then adjust the rest of the system gains to compensate.