I am also having the same issue. The unit was not reading the vehicle, so I went to update bia the MaxiLink software. The unit now is locked on the "PROGRAM MODE See User Manual" screen. Leaving the battery disconnected for a day, holding down buttons to discharge capacitors, and reflashing the firmware with the .bin from the website all do not remedy the problem.
I have just installed Maxi-Link II on another computer and everything appeared correct during software and driver installation. The program acted like it was reflashing (Communicating, Erase flash, Communication..., Update done messages - no errors) was complete. The screen on the MS609 indicated "Program Update has been done!", but after restart, the same "PROGRAM MODE See User Manual" message is displayed.
Is there a previous firmware .BIN I can try to see if the one included in the download (http://auteltech.com/u/cms/www/201304/MS609%20update%20pack.rar) is faulty?
If not, I will need to arrange for an RMA.