I am aware of virus checkers and even more likely windows (pointless) file indexing. I have tried disabling both ( on W8.1) and I still have the same problem from time to time. Even though it affects random files, once it occurs it hits the same file over and over, if I delete the file it moves onto the next file in sequence. I have been in computer hardware and software for decades and this just FEELS like an unhandled error path to me. I run all sorts of file heavy processing on many computers, compiling, photo processing, video processing, data scraping, hard real time........ on Linux and windows and others and this is not a common occurrence (except with windows file explorer). There is something that PI is doing in the image integration that is not handled quite right.
I am trying to find a repeatable, testable scenario, and will of course post it if I mange to do so. Unfortunately it is the nature of stacking that we have quite a few files in a stack so pinpointing the offending combination is tricky.