Okay I think I found the issue, of which I'd be curious to hear if NI has anything to say about it. The issue is with getting the references to the controls and indicators. On RT there is no front panel, so getting references to those controls isn't possible. But the normal way you would do this is to use the Front Panel Property on the VI. Reading the help is says it is available in Real-Time OS...but there is no FP in Real-Time...so it returns an error...so is this really available if it will always return an error? Seems like these two things don't agree.
The reason this didn't return an error is because of a bug in the following VI.
\FPPublisher\WebFrontPanel_class\WebFrontPanel_Create.vi
The two for loops return references and errors, but if the loop runs 0 times (empty arrays) then the input error is cleared. This should either be changed to shift registers, or add the incoming error to the merge errors already in the VI.