I don't know what year LT you've got, but some of the earlier years had incorrectly sized screws holding the changer together. If they are too long, they don't work properly and can cause excessive skipping. There is also a 'setup' screw on the unit that is marked for vertical (car) or horizontal (bike) installation. These have been known to be incorrectly installed. These procedures are in the Hall of Wisdom Troubleshooting - Radio and Optional extras section.
What else I found:
1. Clean the unit with an inexpensive CD cleaner disc regularly. The LT environment is not as dust free as an automobile. This is especially true on the stingray unit.
2. Check your suspension settings and wear. My skipping went to almost 0 when I replaced the stock shocks and set up my suspension settings correctly.
3. As Joe said, check out an MP3 player to replace the changer. You get a sizeable amount of bag space back by removing the changer, they don't skip, and many more tunes will be available. Personally, I went to XM radio on my bike and don't miss the CDs at all.
Get busy livin' or get busy dyin'!
2003 BMW K1200LTC "El Gato Grande"
1993 Suzuki GSXR1100W
1978 Suzuki GS1000C 'Project'