Irregular comms between 32U4 and Processing - "mostly" works.

Please post complete code (or a minimal version that exhibits the behaviour; most of us don't like digging through massive codes).

Please post links to 3rd party libraries that you use (if any).

You use an 32U4 and a CP2104. Is the CP2104 connected to the RX1 and TX1 pins and do you use Serial1 for that? Your snippet does not show anything related to that except for possibly the ComLink which might indicate the use of SoftwareSerial which in that case would bring the question why you use SoftwareSerial on a device that has an additional serial port.