The files that fail to upload with 'rclone' also fail with 'mega-cmd' and after several tests while examining the proxy logs I came to the conclusion that this is a squid/proxy problem, as I see the same messages mentioned in these posts:
https://squid-users.squid-cache.narkive.com/p4ZsWTd5/tcp-miss-aborted-only-with-some-sites
which seems to be site specific (that explains why I don't see these errors/timeouts with the other remote (pcloud).
Thank you guys for the help and for supporting this exceptional software!