The red & green LEDs alternating at about 3 times per second means some kind of internal fault (invalid memory access, for example). When that happens the only option (as you've discovered) is to un-plug the PMDX-411 from the USB port and exit Mach4. Wait 10 seconds to make sure our plug-in shuts down. Then plug the PMDX-411 back into the USB port, wait a few seconds and then re-start Mach4.
(1) Does this happen every time?
(2) Does this happen at the same place in your GCode file?
(3) What version of Windows are you running (XP, Win7, 8, 8.1, 10)? And is it 32-bit or 64 bit?
(4) To help me figure out what is causing this, please enable our plug-in's debug log as described in item (4) of the SmartBOB FAQ here:
http://www.pmdx.com/PMDX-Forums/index.php?topic=75.0Enable the debug log as described, exit Mach4. Re-start Mach4, load and ruin your GCode file. When you get this error condition, disable the debug log as described in the FAQ above. Then create a "profile package" as described in step (8). Send me *BOTH* the profile package *AND* your GCode file. You can either post them here on the forums, or you can email them to be at bob at this domain.
Bob