That is normal.

Sometimes things get confused for LimeWire, and that is where the settings and configurations for LimeWire are stored.

When you delete the .limewire folder, you get rid of that confusing information, and when you start LW it creates a new .limewire folder, so all the settings and configurations are new and fresh. This way LimeWire will not get confused and do the wrong things, that created the problems to begin with.

Hope you understood that.