I'm sorry for the trouble. This is likely a known issue. I believe your processor is in 'factory test mode'. (also referred to as 'debug mode') There is a simple fix for this.
The way to confirm this is to send a simple serial string of "IP<CR>" (use the carriage return of your serial program).
If the system responds with "CMD SUCCESS" then it's in factory test mode. This mode disables RS232 control and can cause the system to reboot on certain commands. SoIP and other external control would continue working when this happens.
I've attached the official procedure for taking this out of factory test mode, which includes instructions (PDF) as well as firmware files that will allow the processor to exit this mode.
This firmware being on '0.00' is often just a result of a recent network change. Often, you would just need to close and start ControlSpace Designer back up. However, if this continues, we have a backdoor firmware updater in our bin folder you can try. Listed as "CSUpdate.exe"