Hey there, I think I found a bug.
Log + Craft file (though I don't think that it's dependant on which vessel it is, but I only tested it with this one, so here you go): http://azzurite.tv/bugreport.zip
Activated Mods:
FMRS
RecoveryController
KSP Toolbar Plugin
ToolbarControl
ClickthroughBlocker
KerbalEngineer
Reproduction steps:
Get the spacecraft launched and out of the atmosphere
Go away from the spacecraft to the space center to check on something real quick
Go back to the spacecraft
Enable FMRS again
Seperate a stage
Land it & Recover it
Go back to the main spacecraft
The landed stage has not been registered as landed, it's still there as if it had not been landed
So it seems as if FMRS just doesn't work when you re-engage it in-flight. I have reproduced it two times, once with all my mods, and once with only the ones posted about here. It worked fine with the same spacecraft without going to the space center.