as far as I can see all transactions are confirmed...how to figure out if there is any old unconfirmed transaction?
You'd need to know that you are missing a specific payment or a TX ID.
Looking to the future, is there anyway you can get these transactions bundled together? I assume it is an automatic payment from some activity... can you set the payment threshold to something higher, so you get say 10x 0.01 BTC payments instead of 100x 0.001 BTC transactions?
A higher threshold is usually a good idea, yes. On the other hand it is still possible to get 0-fee transactions confirmed. I recently saw one that waited 266 days for a confirmation. It will probably take even longer now.