The latest FC5 update is "system-config-kickstart-2.6.6-3", whereas the previous update was "system-config-kickstart-2.6.6-4" . As Epoch is not set explicitly, it seems that this update cannot take effect under "yum update" ...
system-config-kickstart-2.6.6-5 has been pushed for fc5, which should resolve this issue. If these problems are still present in this version, then please make note of it in this bug report.