I've got this to work so I'll answer my own question. I believe that when you click scan for programs this should find programs and make the list for you. On my unit is just hangs (for hours). I suspect it might be looking for a windows program which is missing. The manual way of doing this is:
In PRIMO\save\userlists create user_program_list.txt and manually add the files you want to execute. This will be copied to PRIMO\save\profile\01\userlists and that will be the files edited from then on (or which ever profile your using). I assume the first is the master if you reset data. I guess you could go straight in with the file in the profile. That is the one you need to edit in the future as changes to save\userlists\user_program_list.txt have no effect after the first time.
The format in user_program_list.txt like this
Backlight;\\ResidentFlash\\apps\\BacklightCTL.exe;PARAMETER;0
where PARAMETER is any parameter to give to the program or blank, the usual case, i.e.
Backlight;\\ResidentFlash\\apps\\BacklightCTL.exe;;0
You can edit the program name (e.g. Backlight) and the parameter inside of Primo but I couldn't see a way to edit the path. I assume it expects that to come from a scan (if scan worked).
And in user_program_list.txt this also worked
BacklightCTL;\\Windows\\BacklightCTL.exe;;0
BTW I found that by switching usb mode to ms-activesync I could see the windows directory and files in there. In USB storage mode I couldn't see the files in \Windows only in \Resisdentflash.
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