Daniel,
I've been testing/refactoring my interface module for the RX-AxA series, which is ONLY IP controllable (IR of course) and I have not had any connectivity issues that you describe.
I'm holding the CONNECT input high just after program start, and I've had good luck with reconnection after program updates/processor reboots, and even when I mess with the Power and network connections of the AVR.
For Previous Yamaha AVR models, I was using the RS232 module and connection with no issues.
Though it could be the older models that aren't as reliable with IP, OR you might have something going on with your network...
