That is unusual that JSGME did not remove them. Did the MFM overwrite anything when you applied them? Mine went in clean, overwritting nothing. Of course that is as it should be. MFM alters nothing and only adds the ships.
I've found it best to have JSGME set to
Rollback on Exit.
In the past I have forgotten to do a rollback..added something with JSGME and confused it all to heck. Sometimes beyond redemption...
