gwarder,
Next created a Dual FFT Analyzer. In the bottom drawer I set the source to the appropriate Apollo 16 input. Under the "Excitation" tab, I Selected the appropriate output channel...sine sweep...Logarithmic. I left all other settings at default.
Did you select the same (excitation) output channel for the Reference input (next to the Source input selection)?
Next I selected Control->Start All Tools. I confirmed that I could hear the repeating excitation signal in the room and that the mic was picking it up. While the excitation signal was in progress, I selected Control->Capture all Data. Then I stopped all tools.
If you have any other tools in your project, I would recommend just starting and stopping the DFFT Analyzer directly, rather than all tools simultaneously. Also, for room measurements, you might want to set the averaging type to Linear and let the analysis complete (and stop on its own) before you capture the data. (The default number of averages, 10, may be overkill, but it won't hurt your measurement.)
Also, before capturing the data in the DFFT Analyzer, I would recommend that you inspect your measurement data to be sure it looks right. If you are familiar with ETC or squared impulse response curves, I would recommend that you select the Squared IR function in the Display tab and make sure you see the kind of acoustic decay you would expect in your measurement. If you don't have valid measurement data in the DFFT Analyzer, you can't expect to get meaningful results when you load it into the Room Analyzer.
The Coherence function can also be used to verify the quality of your measurement, as a function of frequency. A coherence of 1 is ideal. The smaller the coherence, the less meaningful your data is at a particular frequency.
Ben