Duplicate Menu entries and JS errors

Well, in between I have installed R1.3.1 - and this one works w/o a problem. No duplicate entries, no JS problems... Until you solved the issues I experienced or tell me how to avoid them I will stick with 1.3.1 on this server.

Problems solved, thx to wjames. ,)
I made a new installation and the duplicate entries were gone (it merely was that bitweaver was missing the icons, for whatever reason).
The JS problem persisted, though. It was because of incorrect chmod settings in 'storage' and 'temp'.
I think it would be a good idea to implement a check for this into the installer. ;)