HDC2460 channel 1 command interfere channel 2

We implemented the channel 1 as a steering motor(close loop count position) and the channel 2(close loop speed) as the main motor. When we send a command like
!s 2 50 and follow with !p 1 1000 a few seconds later, the command of !s 2 50 will some how execute again itself which is now causing great problem for us. Also this interference only come from channel 1 to channel 2 and never vice versa

It sounds like this is an issue with the watchdog

If no new command is received within 1000 ms (default value), the motors will stop. If a command is received after that, the previous command is awaken too.

For your tests, disable the watchdog by putting 0 in that configuration.