@demands I hope that update allowed you to recognize your Clipper Card with the RFID reader. We've just published a pretty big update to the module library, so if you update through npm again, a lot of the reliably issues @jon mentioned should be cleared up.
As for your Zipcard, if I'm correct in assuming that is the card ZipCar gives its customers, I'm afraid our reader does not support that specific NFC technology. Our reader operates at 13.54MHz while their cards operate at 125kHz. A partial list of card types our reader should support can be found here. The card that came with your module is MIFARE Classic, and your ClipperCard is MIFARE DESFire, so you should be able to read those just fine now.
Feel free to post with any other questions you may have.