My experience with AIB is that it takes 10 days for the cheque to clear the funds even after it shows up as lodged in your account.
If you lodged the cheque with a cashier it would show up immediately as lodged in your account.
If you used the quick lodge machine on a normal day (not around Christmas time) they will usually lodge the cheque at close of business.
Cheques don't appear in your pending transactions, that is where you have used your debit card and the payment is pending.
As far as I know the problems that AIB were having over the Christmas period were only to do with ATM withdrawals.
Might be best for you to [broken link removed] if you are worried about anything.