I've been doing a lot of work lately with my Maple r5 and noticed this rare phenomenon as well... well, it's not that rare -- every single time I want to program the Maple I must perform the button combo, and after a few hours my fingers hurt trying to keep those teeny tiny buttons down.
I've also noticed it doesn't always stay in the "perpetual bootloader mode" every single time. For example, I press the reset button. The blue LED blinks rapidly, at which point I press and hold the BUT button until it slows down in its blinking rate. I switch over to the terminal, hit enter. By the time the make install
gets up to looking for the serial port the Maple exits the "perpetual bootloader mode" and runs the previously uploaded program.
This only applies to when my program is more compelx than the simple "Hello World" included with libmaple. I don't touch any of the "special" USB related pins on GPIOC in my projects, so I'm not sure why this happens.