I,m just a tad puzzled here as my Empeg gets used by my master home system, several other peoples home systems "I do parties as DJ" plus I have some very serious equipment at home and in the vehicle and I don't have any of these issues.
It MUST be the quality of your encoded MP3's. Don't download anything from the net as you can never be sure what you will get (usually crap) I encode all my own stuff at 160-192Kbps with only the Fraunhofer 32bit codec. (The only true codec as they invented MP3... ) other codecs such as Xing truncate freq's above 16Khz and some others absolutly butcher most tracks in some form or another. Remember this, if your encoder is of the 'fast' variety then it's most likely doing a crap job. Encoding a quality MP3 takes time. if your going to keep these files for life then do them correctly. if your just gonna play on your pc through some small crappy speakers then use Xing or the like. Good things come to those who wait!
My player sounds excellent in all cases!!

Don't forget your CDROM..... I have used some that do not rip digital direct correctly - usually cheap-o IDE drives.
If you use the Plextor Ultraplex SCSI drives you will not have these issues. These drives were designed with digital ripping in mind.
Barring all that, your players outputs may be wounded or your Stereo's inputs have some other odd troubles.
The purpose of my post is simply to state that the Empeg should sound very very good. If it doesn't, do not think it is the norm or should be expected. The empeg player sounds as good as any of my high end equip.

as usual...... My 2c.

12Gb MKII 080000516 Blue