I think the problem is caused by the Jaguar having one or more bugs in the UART. This is also the reason why so few Jaguar-games offer networking modes. AFAIK Atari wasn't able to provide 100%-working workarounds to the developers, look at the problems of the 2-player-mode of Doom for example. Sending from the Jaguar seems to be no problem, but receiving. And at that point the Lynx comes into play: The Comlynx-port is designed as a single-data-wire solution, the 2 signals Rx and Tx are connected. So you need to care about this also when developing a Lynx-Jaguar-network (hw+sw).