I run EasyBCD from a shared HDD where it sits in a folder with other portable and legacy programs. I haven't tried running it from a USB stick, so have no experience of any such problem, but you could try it on a different stick to see if it's the particular h/w that's giving a problem.
I only mention it because this week, my PC seemed to be completely borked and unresponsive and it all came down to one old 8Gb stick with music files on it which was screwing the entire PC.
God knows what had happened to it, but even attempts to reformat it crashed the PC.
It's now gone for recycling.