I finally got tired of this one a while ago and implemented a change (with my Meteobridge setup) that is essentially:
1) Change the upload file name to {tagfilename}-new.php.
2) Implemented code (in top.php and my METAR cron job) that looks for a '-new' file newer than the current tags file and of reasonable size. If so, copy the new version to the tags file.
I haven't seen the issue since.