Whenever I start Limewire for the first time that session (ie, after I've turned my computer on) it will load all fine, display the whole interface and even show the "upgrade to pro" nag thing, but then it will just disappear. The window will close, the icon in the system tray stays but only until I mouse over it and then it disappears too, and then I have to load it up again. Why does it do this and is there anyway to fix it? My Java is fully up to date and so is limewire. But that doesn't seem to matter anyway as I have had this problem for a long time. (been through many updates of both java and limewire and still the problem persists)

Have you tried Java 1.6? Use the JRE offline installer & remove any old Java versions before installing the new one.
http://java.sun.com/javase/downloads/index.jsp

Delete LW's preferences folder when LW's properly closed (check in task manager). See points 2 & 3 below. If you've used LW versions older than 4.9.34, you might have a folder in both locations. If you've only used later versions, just look in point 3's location.
Fixes for LimeWire

Also try changing compatibility (point 5 above).

Otherwise, check to see that LW's on the list of exceptions/allowed apps for any antispyware & security programs you're using. Some people have had trouble with their antispyware seeing LW as a threat & preventing it from opening/running.