Why are you rewriting the multi-span example? NI-RFSA 1.5 installs a new set of LabVIEW driver VIs for the PXI-5660. They add multi-span capabilities automatically such that requesting a 100 MHz span, for example, results in 5 20 MHz chunks being acquired and concatenated automatically. In addition, programming the PXI-5660 is far easier with these VIs in general.
The VIs are installed into the Instrument I/O->Instrument Drivers sub-palette in LabVIEW.
As for the HW, yes - requesting a smaller span of frequencies (<= 10 MHz) causes the PXI-5600 to tune in larger increments (5 MHz). This is not a function of software, as the software is written as a function of the HW. If you want to force best phase noise, go into the code for the ni5660 Configure for Spectrum (NI-RFSA 1.5), look for the code inside the FALSE case of the case structure (which is for multi-span), look for the niTuner Set Freq VI and wire an array of spans whose length is equal to the length of the frequency array and whose elements are all values <= 10 MHz.
This is not recommended and any problems incurred as a result of changing the default behavior of the instrument will not be supported.
You can install NI-RFSA 1.5 from here:
http://digital.ni.com/softlib.nsf/websearch/C1A9A160FA5AD89B86256ED8005E0761?opendocument&node=132060_US