What version of rtd explorer are you running? it doesn't sound like you have the latest version. it shows the version in the lower right of the screen. Latest version is 0.3.1.45. Try updating RTD explorer. If the updater doesn't work go to
www.EVVette.com and download the latest version.
What version of the firmware do you currently have on the controller?
It sounds like you have an older version of the firmware that doesn't support automatic restarting. Do like you normally have been, but when it seems to hang, restart the controller. This should trigger the bootloader on start and start loading. Loading should take about 40 seconds total to be done. Data will also be flowing int he terminal window while it is loading.
Let me kno!!
-Adam