Do cFP modules have to be in place when the unit is initialized?

Running:
cFP-1804 backplane over serial connection to Mac OSX via a keyspan USA28X, using a legacy VI that has (up until now) been used with legacy FP system (FP-1000, etc), also serial.
cFP-AI-110 measuring 1 - 10 V at 1 input
cFP-DO-400 sourcing 24 V to four channels out
cFP-AO-200 sourcing 4 - 20 mA to 1 output
The modules are in this order on the backplane, with the farthest slot from the head being empty
After tracking down a Windows box to use MAX to initialize the unit, I connected the unit to the Macintosh that is running the VI to find that only the DO and AO modules function as expected. I measure a voltage between pins 1 and 18 (COM) with a voltmeter, but no such measurement appears on the front panel of the software.
Interestingly; I tried moving all of the modules over one space to see if the position on the backplane mattered, and lo! the control that is supposed to actuate output 0 on the AO card actually punched on the DO output. But still no voltage measurement.
So, the question: If modules are connected to the cFP-1804 when it is initialized, or the firmware is flashed, does this mean that the units are no longer interchangable? Would re-initializing the unit with no cards inserted allow none to be recognized?
Also, I have noticed that it takes a particularly long time for the system to come on line once the VI is started (10-15 seconds). Could this be related?

Here is some references for Optomux Programming:
FieldPoint Optomux Programming Reference Help
http://digital.ni.com/manuals.nsf/websearch/A62558E5BDED8486862573460055DF12
How Do I Effectively Use the FieldPoint Optomux Commands?
http://digital.ni.com/public.nsf/allkb/3EC99318D768D87E86256E0D007FBFEE

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Do cFP modules have to be in place when the unit is initialized?

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