Sorry I can’t provide more help.
When you automate opening the files, doing something to make them "dirty" (add a layer and remove it for example) and saving them are those files accepted by your server software?
It’s not proper but if it is really important to your workflow maybe you could try contacting one of the Adobe employees who participate in the Photoshop General Discussion Forum via privat message.
I’m not sure they could solve the issue (as the files work in Photoshop they would appear to both be in order, but sometimes file formats can allow for ambiguous data supposedly); they might be able to pinpoint the difference, though.