Apparently the real robot you took the backup from had its ext.E-stop connected through Safe I/O Connect, and thus that setting is apparent also in Roboguide.
Your way of doing it is one of the ways to overcome your issue.
Basically, the vertical controller does not recognize a signal coming in to the SSO[3] through either a Safety Fieldbus or an additional safetey I/O board (why would it?). But by removing it from any declaration or setting, it will assume that this signal is instead hard-wired directly to the e-stop board. By default, this signal is jumpered.
I bet there are ways of connecting a virtual controller to some kind of I/O-bus to be able to fully simulate a robot system (with safety I/O and all), but I've never tried it.
When working on roboguide, just after creating the station from a backup I usually reserialize the robot and remove the DCS option from the controller, so it doesn't give any errors or emergency stops... or any other things.
If you will not be adjusting any dcs zone previous to loading and checking it on the real controller, I recommend you to do that, you will avoid the pain of bypassing the dcs all the time. Also you can add the IRProgrammer option on the robot and use it to code easier than with the virtual TP.
