spoekes, I think there's some confusion as to what's causing the problem. I found, as per the topic you linked, that the problem with installing 3.2 lay in Rockbox Utility not saving the Rockbox bootloader as PP5020.mi4 to the MR-100's /system/ folder. After rectifying this situation I was able to load Rockbox 3.2 without trouble.
I do not know why installing Rockbox 3.1 via the Utility works for you.
I posted a bug report at FS#10225 detailing my findings regarding a missing PP5020.mi4 (only OF.mi4 present) after telling Rockbox Utility to install the bootloader. Exactly what did you do to install Rockbox 3.1 versus Rockbox 3.2?
Edit: See the task at FS#10221 instead. I should have searched before posting.