This is expected behavior for the module. The communications link watchdog is a safety feature that allows you to set the outputs to known values when communications with the controlling system are lost. Thus, when communications are resumed, there is a need for the FP-1000/1001 to let the control system know that it had gone into watchdog mode, the first command it receives following the watchdog timeout, generates the response string "N06" (see FP-1000/1001 Progammers Reference Manual page 2-3) and ignores the command. Subquent commands that are received will execute normally (until another timeout occurs). What you can do in your code is to look for the "Communications Link Watchdog Timeout Error" to know when the system went into the watchdog mode. At that po
int, the system outputs may be out of synch with what the computer thinks they are (since the FP-1000 will change the states of any channels that have the watchdog enabled), so you can then initiate some sort of re-start/re-synch sequence in your code.
Regards,
Aaron