I experienced this same issue.
I had my backups set to start at 9pm, then switched them to 6pm. I noticed that they would run twice, (once at 6pm, and once at 9pm).
me@server1:~$ sudo crontab -u ebox -l
0 21 * * 6 /usr/share/ebox-ebackup/ebox-remote-ebackup --full
0 21 * * 0,1,2,3,4,5 /usr/share/ebox-ebackup/ebox-remote-ebackup --incremental
me@server1:~$ sudo crontab -u ebox -r
me@server1:~$ sudo crontab -u ebox -l
no crontab for ebox
I am very sure this will remove the 9pm backup process, but I'll be sure to report back if it doesn't.