Ok, there are a few things going on here. I'm not actually sure why it says the right electrode has 23 atoms, it's a bit odd. But the bigger problem is that have forgotten to use k-point sampling the y direction. I think this is the reason why your system in the end goes crazy - in fact in the last iteration you have no electrons anymore in the central region, and then all kinds of odd things can happen, like you get very large forces (look at the Forces report in the log file!) and atoms move to weird positions.
But, I also don't quite understand the line "Forces step = 107" - did you cut only part of the log file?