I have a few FWSM contexts (Version 3.2(7)) which always appear in the Startup and Running Out-Of-Sync report.
The obvious reason is, that the "show running-config" command on the FWSM hides "asdm" commands, while "show startup" does include them.
IMHO, hiding commands from "show runn" is an insane idea in the first place. But I don't think I have a chance to get this fixed.
RME should cope with this problem, anyway.
The obviuos workaround would be to use "show running-config all" to archive the uncrippled running config.