Just in case it's of use to anyone in future:
We found that even though the MIDlet-Name and MIDlet-Vendor fields were identical, a change to the 'codename' passed to rapc.exe also resulted in the RMS Record Store being lost. This affects various JAD values (RIM-COD-URL-X, RIM_COD-Module-Name, etc) as well as the name(s) of any COD files.
In our particular case, the only change was the capitalisation of the name.
