I haven't used Tuneboy in years. The old versions I used were not too difficult. Tuneboy should have more capability than TuneECU.
I just went on the Tuneboy web site and looked at the tutorial for hooking up. It looks like a colossal hassle. You have to get it connect, download a tune to prepare the ecu, turn off the program, turn it back on to enter your pass code, turn it off, then turn it back on to load your tune again. Did you do all that crap? If not, it's no wonder you had problems.
TuneECU is pretty easy and the same stock tunes, plus a lot of custom tunes, are available.