Three points:

1. Try not to use place-holders for updates. In my experience, the biggest performance benefits for placeholders are in updates and inserts, not in selects. Not only that, I can't count the number of times I've screwed up quoting on different DBs. That doesn't sound like your problem here, but nonetheless you'd be well-served if you started getting into the habit of using place-holders everywhere.
2. Just because you are logged into a machine as root doesn't mean you are logged into the database as root! You need to know what your DB login is, and what privileges you have on the db, not just on the OS.
3. It's hard to figure out what your problem is without a little more info. If you can, please give us the OS, MySQL version, DBI version, DBD version, and the script (remove passwords certainly, and feel free to change table-names to something like table1.field1). Finally, we'd really need to see your SQL to say much more. If possible, post the DBI trace log and that will help us a ton.