I recently used online check-in (for a different airline) and printed off our online boarding passes for the flight. Great!
After standing for ages in a queue at Security, the bar-codes on our boarding passes were scanned, and promptly rejected by the system. So I had to go back to re-join the queue at the check-in counter, do a swap for the normal type boarding passes, and queue again at Security.
In future, I'll always ask for normal boarding passes at the baggage drop-off desk!