Since x11-misc/xfce4-notifyd-0.1.0_p20090722 returns version string as of 0.1.0git-20090607-3ea7a2e4 gajim does not understand it and assumes that notify daemon is broken, hence notifications do not work.
Created attachment 204838 [details, diff] A patch which more or less addreses the problem. Patch should work, but I never tested it with x11-misc/notification-daemon, so corrections might be needed.
Patch is included in gajim 0.13, marking this as WONTFIX, since priority now is getting 0.13 in the tree