i have one server that has the same issue.
configuring the cron from cpanel produces a file in /var/spool/cron/USERNAME , but with size 0
transferend accounts (to that server) have their crons in place, but if i try to modify one working cron from cpanel it gets erased and zero-sized again.
I haven't found a fix for this, therefore i edit the crons by hand. Funny thing is i have many servers with almost the same setups, and only one has this problem.
And its' true, upcp, with/without --force doesn't fix it.