I recently installed BackWPup and have gotten it to work for WP export, Database and Files before.
I created a new job to run weekly that backs up the first three choices (WP,Database,Files) but got the error below near the end:
2013/01/15 16:09.20: [ERROR] Zip archive create error: PCLZIP_ERR_MISSING_FILE (-4) : File '/home/sugarmtn/public_html/wp-content/plugins/si-captcha-for-wordpress/captcha/temp/1TGebtJcy2G2ANVZ.php' does not exist
Right after that error was the warning:
2013/01/15 16:09.20: [WARNING] filesize() [function.filesize]: stat failed for /home/sugarmtn/public_html/Backups/backwpup_3_Weekly_WP_DB_Files_2013-01-15_16-05-48.zip
Since the backup has worked before both doing it through CPanel and through BackWPup I suspect that the file not existing isn't what it is really trying to tell me since that file is there.