I don't see any code added in the patch that should interact with live errors.
In 25.0.9-gold, I had set it up so my default live errors for python was wrong, and added a entry in the Project Live Errors to use the only pylint I have installed currently. Verified it worked, and then switched to the patched version. I had what you saw happen only one time, but haven't had it happen again. So there is something weird going, but I don't think it specific to the patched version.
I'm going to mess with it more and see if I can find a way to make it happen again when I have a debugger attached.
So I'm going to guess it might work for you if you try the patched version again. If not, check your se.log and see if anything dribbled out on stdout/stderr. (not expected, but not impossible). And if you can reproduce it consistently, maybe give it a run under strace and look at the execve() calls to see if any are for pylint, if they're for the correct one, etc...