Its an educated guess. Based on the fact its only when the file is no longer available in the temp directory, and that it can happen even if the file is still open.
Typically if I have 20 files open, if I leave them for 20 or so minutes, they will all be "deleted". This will cause about 1-2 minutes of clearing error messages before continuing with whatever I am doing. If there is an error message up even if I have a file up that has not been removed, it will not be uploaded until I clear all the messages, so if it happens every 20 minutes it causes roughly 6 minutes of down time every hour to clear the messages.
Also if I have many files open and everything is fine when I am done and close it. The next day when I return to work on anything again I will have to clear error messages as soon as I open the program.
Also one other odd thing, the error messages do not trigger it to alert the user, in some cases, like when doing anything with WinSCP, it will change the icon color to "orange" (maybe different colors depending on windows settings, not sure what this functionality is called). Basically to alert the user something might be wrong. This functionality does not happen with the "code 5" error, making it impossible to know if the error is preventing you from uploading files until you actually open up WinSCP.
I have been working with WinSCP for years and have usually just dealt with this issue, so I believe at least version 4 to present this has been a problem. It has happened on every computer I have used it with, that is with sublime text 2 as the editor.