Currently we have not contacted NI. As we figured well it still works its not broken just a little confused if it wants to be safe.
As for the dip switch we are fine as long as there is no rule stating the crio safe mode having to be in the "OFF" position.
But for having to physically press the reset button on the controller now thats a problem for NI. Will contact NI and post a reply for all those with similar issues.
Just glad we aren't the only ones with this issue.