Odd behavior of Leonardo-compatible after accidental short

Hello! I accidentally shorted the 5V pin of the voltage selector pins on my Olimexino-32U4 while the jumper was set to 3,3V. The board still works, but from time to time the Arduino IDE tells me that the COM port is already in use. It also has created a load of com ports, two for every USB port it was connected to, it's seems to be random ranging from COM6 to COM11 now depending on which USB port it's connected to. It's a little bit like playing the shell game to get the right one then :|. It's the same issue in Windows and Ubuntu. I reflashed the bootloader, but that did nothing. The odd thing is that it's acting completely normal again as I write this. I'm a little bit afraid that the ATmega has been somewhat damaged. SMD soldering would be a torture with my club of a soldering iron! Does someone have an idea what could be causing that (Except for the short, duh :))? That's so odd, I'm actually smiling while I'm writing this XD.

Edit: After some hours of coding and playing around it seems to be back to normal, even the code that caused the most issues is working perfectly :astonished:. I would still like to have a guess on what could have caused all that.