it's because you're using a mysql backup tool!
http://www.pantz.org/software/mysql/mysqlcommands.html[mysql dir]/bin/mysqldump -u username -ppassword --databases databasename >/tmp/databasename.sql
or if you're using winblows, windows key +r, cmd, go to dir of backup, assuming mysql bin path was added,
mysqldump -u username -ppassword --databases databasename > backupname.sql
clean and simple, can set up a scheduled task or cron job to auto backup too!
Though, I'm guessing your mysql admin tool does that already.
I'm confused how running a backup screwed up in game though, unless it's locking a table during the backups.. eep!