Could it be that your temporary file folder would get emptied while KNIME is closed or that it is at a somewhat unstable location.
Then you could try and start KNIME with the -clean option on top of the knime.ini file once.
The do you have the files in a folder that would sync with Dropbox or OneDrive?
Maybe you could set you log level to debug, clear the log and start KNIME again to reproduce the error and than share the log with the forum here.