Chris,
Do you happen to be interfacing the JMRI computer to the DCS52 via the DCS52 integrated USB interface?
I ask, because several DCS240 users, including myself, have experienced some instability of the DCS240 USB interface. When issues occur, the symptom is often that the USB interface is "locked up", and the obvious workaround is to quit the program, disconnect the DCS240-to-DCS52 USB cable, power-down and power-back-up the DCS240, re-connect the USB cable, then re-start the computer program.
An alternate workaround is to connect the DCS240 to the computer using a separate interface device (PR3/PR4/LocoBuffer/LocoBuffer-USB/etc.). This solution has worked well for me.
Regards,
Billybob