The GUI uses the position of the UPPAAL jar file as a landmark to fine the server executables. In 3.6 beta 2 the jar file was renamed from uppaal2k.jar to uppaal.jar. However, the GUI still searches the class path for uppaal2k.jar to find the server. Hence, the GUI cannot find the server binary unless the current directory contains the bin- directory or the server path is explicitly given on the command line. A temporary workaround is to rename the jar file from uppaal.jar to uppaal2k.jar.
Fixed on the trunk from rev. 1709.