That's very good information, thank you! I kind of suspected this was a dead end. There seems to be a lot of potential for higher loop rates on the cRIO and this is an interesting thread related to this subject.
http://forums.ni.com/t5/LabVIEW-Embedded/cRIO-Poor-Performance-Where-have-my-MIPS-gone/td-p/3026371
Set the front panel window to the window to hidden using the Invoke Node on the VI class (Front Panel >> Open - State). And in your built EXE you may need the HideRootWindow = TRUE in the INI of the application.
My LabVIEW Tray Launcher uses this code to be minimized to the system tray, you can checkout the source here.