So is the OTAP command taking control of the port in some way? Or reconfiguring it? I'm a bit confused.
When you use OTA, it takes control of serial port, but when it finishes, serial port is liberated, so your issue is quite strange.
You can test it using Waspmote IDE for example, if you plug the gateway you can see the corresponding serial port on tools/serial port. then, if you run OTA, you will notice that serial port is not shown on IDE while OTA is running. When OTA is finished, serial port is available again.
We will think in your issue. In the meantime, can you give us more detail about this? How do you parse, etc.