Per your private mail request in order for your team to troubleshoot the USB programming port issue found in my private laboratory, please find the link to a simplified Serial Protocol between any arduino (UNO, MEGA,...) and a Java GUI which has been running on PC and Mac for years in my power electronics open sourced projects (ferro-resonance and plasma-resonance).
You would need only wire 4 LEDS on pins 24, 28, 32 and 36 each in serie with 1K resistors in sink mode
to verify that SerPro for some reason, does not correctly communicate with java GUI on my MacBook Air and iMac.
LED24 for LinkUp
LED28 for CRCerror (HDLC with 16 bits CRC)
LED32 for Xmit data
LED36 for Rcv data
When the link is first correctly established, LED24 will stay ON then using the left two GUI slider will make blink LED24 otherwise, using the right sliders will make blink the LED28.
P.S.1. Prior moving any sliders, the Java GUI will receive from arduino then display some PWM frequencies and duty cycle, namely 24450 Hz, 37%, 10%...
P.S.2. After using left sliders, LED24 will then always stay OFF except when moving left sliders
One example of very complex use of multiple timers on arduino MEGA along with homemade FPGA's being isolated barrier from more than 7000 peak of reactive power (loose-coupled Hartley oscillator), please see this specific video on my YouTube channel
When compiling and downloading my arduino DUE the IDE, everything goes OK except all the LED's keep flashing hence serial HDLC link is never established, many CRC errors, constant Xmit and Rcv for ever.
Thank you in advance for your time, Albert