That is true, it could just be the 1k/4k thing and it throwing a bit of a tantrum. [Could it not just get detected by checking manufacturer data? Kinda like Taginfo does it, it says “unknown Mifare manufacturer, possibly cloned”.] That could probably explain the delay, and the breathing lights could be like a HDD light. The curious things is that they just don’t stop. Will have to observe further.
The reader definitely connects to the server, since there is no localy stored data either on the card (there is only a birthdate, card validity, UID, enrollment number) or on the reader/printer itsself. There, it checks the account balance, and allows you to securely print your files that you previously sent to that server through a web interface.