I don't think it's "messed up," IIRC in 3.4 KDM disables root logins by default. You can change this by editing the /etc/kde3/kdm/kdmrc file. Look for a value called AllowRootLogin, and change it to "True."
Also, lardman notes that they will be "locations under /usr," not the /usr directory itself. Lots of times locations like /usr/bin and /usr/local/bin are part of the $PATH variable, but /usr itself is not. If SuSE installs multisync to /usr/local, your best bet is to leave any related files in /usr/local as well.
Your bestest bet is to go to a package manager (YaST in SuSE I guess?) and see where the plugins that come with Multisync, or where the plugins that you've installed from RPM packages, are installed, and move the GPE plugin there as well.