Just wanted to Update. I got the board in the remote replaced, I do feel the remote connects much better now. This issue did not go away with just that.
I kept trying things and found the problem. In my POWER ON macro one of the commands is to Power On (RS232 command) a Yamaha RX-V3800 Receiver. I decided to remove this command. The macro worked, then connected an IR cable from the Serial Extender to a direct IR input port on the receiver. I added in the IR Power command and have used the remote for a couple of weeks. The macro
works perfect every time. I have no idea why the RS232 command was causing the issue and forcing a reconnect for the remote but it seems it was the fault. I have no problems controlling the Receiver with RS232, only during the Power On
macro.

Anyway all is working.

Thanks