Hello!
You say that you can only see the top of the window maybe you just could try dragging it upwards and it will display the entire content. If this does not work then it could be related to the following:
-Corrupted preferences. Try trashing the .limewire folder found inside the System Folder inside the program preferences folder and re start your Mac. Then try to launch LW and you will be taken trough the set up wizard. And it should then work if this was the issue.
-Java problem. Maybe are you using a version of MRJ that is to old. Update to MRJ 2.2.5 if this is the case. And assign it 32000 as the maximum value but dont touch the minimum value. To assign memory to MRJ do the following Highlight the original application icon and from the file menu select Show Info >memory and set the maximum value to 32000 then re-start your Mac for the changes to take effect. You dont have to assign more memory to LW itself since LW will do that automatically since it is a Java app and works differently that way compared to other Classical Mac OS apps. Anyway after you have installed the latest MRJ and assigned it proper amount of memory you should uninstall everything LimeWire on your System. Just use the Uninstall app that was included with the LW install. Then use Sherlocvk and search for LimeWire and see if it finds anything left and if it do just trash the rest of the files except the Shared folder ofcourse. Then download a new copy of LimeWire 2.9.8 and install it. Found here:
http://www3.limewire.com/download/2.9.8/