1. From what I have seen, this error is usually caused by one of two things. The first is the Shared Variable software components not being installed, which is covered in this Knowledgebase. The other is due to a corruption of the ni-rt.ini file on the Real-Time controller. You can follow the steps layed out in this Knowledgebase, which gives three possible remedies. You could also try reinstalling the software (firmware) or create a PXI Uninstall disk from Measurement & Automation Explorer by selecting Tools»Remote Systems»RT PXI Disk Utilities»Create PXI Uninstall Disk. Boot the PXI Controller from the PXI Uninstall Disk, which will erase the ni-rt.ini and ph_exec.exe on the target. However, you will need to reconfigure the controller after doing this.
2. Due to the nature of the digital I/O on motion controllers, it is not surprising that you are seeing around a 1ms delay. It deals with the fact that it must update the motion controller with the new value on each control loop. This Knowledgebase gives a little more clarification regarding the 7350 specs.
Yes, it is possible to load a non-NI dll onto a RT target, but just because it works on a PC does not necessarily mean it will be compatible with the Real-Time OS. This Knowledgebase contains a utility that attempts to determine whether or not the dll will work in LabVIEW Real-Time. Keep us updated on the results.
The digital I/O is software timed (single point) and can have jitter, even in LabVIEW RT. The update delay also applies to the digital output on the motion controller. Again, it's the nature of how motion controllers update the digital I/O bits on each control loop. Are you wanting to do Pulse Width Modulation with the DIO?