We have found the fix to this problem thanks to the help of Teradici support.
When you scan a credit card swipe over the WAN using PCoIP it doesn't compress very well. This is the main reason why we would be missing characters in the scan. This problem was not seen when using the RDP protocol. So to fix this it is imperative to bridge the device in the teradici web interface settings.
To bridge you have to go to Info and then attach devices and identify the "VID" and "PID"
Look in the model area to identify your device and then look over to the "VID and "PID" settings and record them. Then click on Permissions and then USB to bridge the device.
scroll down to "add new" in the bridge device area and then add the "VID" and "PID" values. Reboot the PCoIP proccessor and test. You will the scan slow down compared to when it was not bridged and then the scan works. It picks up every character and it doesn't cause the computer to lock up from adding additonal characters at the end of the scan.
I hope this helps other users - Let me know if you have other problems as i would like to see if it fixes it for everyone.
Judah Sameth