At L2, where Sapnning Tree works, the device/switch does not care about appletalk. Without knowing the exact details I can only guess at the problem.
My guess is the issue is probably related to how long it takes spanning tree to go into a "Forwarding" mode. This delay can cause upper layer protocols specially older ones i.e Appletalk, IPX etc to time out before the port gets into this "Forwarding" state. Causing login issues etc
Solutions
1 Use rapid spanning tree (RSTP) instead of standard spanning tree (STP). Its faster so the timeout may not happen
2 Disable spanning tree on only those ports with Appletalk devices