One of my "tools" is notepad, configured with {$ActivePath}. When I try to start it, I get the message:
(file could not be opened).C:\PROGRAMME\SYNCHRONIZE IT!\"\\SOMESERVER\SOMEPATH\foobar.txt" kann nicht geöffnet werden.
For me it looks like SynchIt adds the path to the program itself infront of the files path, if the files path doesn't start with something like "C:\". I think, pathes starting with "\\" should be considered as absolute pathes just like "C:\" and no changes should be applied.