You can imagine that while Limewire is running, its kinda busy downloading, searching, uploading, and keeping connected.
When you use the internal player you are just adding more tasks for limewire to preform, and often it will need more resources, and take from the player, causing clicking, and interference.
Do not use the internal player while downloading, or searching expecially.
I prefer to use Media Player, to the play the file after the file is complete. This frees up resources for limewire, and helps it run faster..
Robley