mine does that sometimes, it is just the keypad getting old and dirt inside it is stopping the keys from registering soemtimes. i disassembled mine and cleaned it and solved the issue for a while, though it is doign it agian now. if you break it, you have to buy a new one, so be careful if you do this.

Mine is brand new and also does that. I found out that if I hit enter twice it works the first time, no idea why but it sure beats putting in the number twice. Also would tell people it is sure worth the extra money to get a keypad entry, would not be without mine :)

Here is a link that might be useful: Barrie Home Inspections

let me know the brand of opener you have. Also specify if this is related to the keyless entry on the outside of your garage.