I had the same problem just watch when you load MRL.comm.ino that you get the right version. My own set up for mrl still flashes the error which states. MRL.COMM.INO was getting version 9 when it was expecting version 13. I still have not cured this problem although it does not seem to be causing me any problems.

Peace out 

Dwayne dwilli9013

I have the same issue on a windows xp VM and like others it does not seem to affect the running of the program at all and seems to clear itself if I leave the program running for a few minutes.

Win 7 x64 on a quad AMD.

Also seem to avoid the issue If I send the Arduino sketch up via the proper latest stable IDE rather than the MRL one.

(update)

Am running MRL on main computer today (not in VM) but all of a sudden I cannot see any com ports listed when I open an instance of MRL arduino IDE. Full arduino IDE sees ports just fine

Just for fun I got latest MRL 1032 and also followed this advice http://answers.microsoft.com/en-us/windows/forum/windows_7-hardware/how-do-i-delete-the-unused-com-ports-in-windows-7/4bb72733-1be0-4168-9ba5-68dcb72d31d9

One of them fixed the issue and I can now see my com ports in MRL again.