russmathis:
Could this have something to do with the interrupt vector routine or am I chasing lost bytes?
Not having ever used this reader, I can't be sure. However, your results do indicate that timing is at least a major symptom, if not the cause of your issue. If you haven't tried the variable delay setting, undo any delay you've put in your code and try that. Other than that, I'm don't think I'll be able to offer much more meaningful suggestions.