I don't think JMRI can destroy the decoder hardware, but it can mess up the firmware. JMRI only sends commands to your DCC command station, which then communicates with the decoder.
Have you tried resetting your decoders to factory settings with CV8=8 (or similar)?
It could also be a problem with a different specification of the number of speed steps (14 or 28/128) between the DCC command station and the locomotive decoder. The digital commands in the two modes are different.
?
@_Uli_