Hi-
I read through the SCXI-1102 manual and it does matter. First off, the 1102 internal MUX can only scan 1->32. If one was to scan 1, 3, 5, etc actually the MUX is going through the even channels too, but that data is discarded at some point.
http://digital.ni.com/manuals.nsf/websearch/2CDD38710DA595BB86257150006A6285
http://www.ni.com/pdf/manuals/371975d.pdf (the actual pdf)
see page 35 "Theory of Multiplexed Operation" for the specifics.
"The list can contain channels in any physical order, but the SCXI-1102/B/C multiplexer can only sequence the channels in the order 0, 1..31. The SCXI-1102/B/C cannot skip channels or scan channels in random order. The ordering of scanned channels must be sequential. "
and
"Since you must scan the SCXI-1102/B/C sequentially, the driver automatically scans channels not included in the scan list if a sequential order is not maintained. When this happens, the maximum sample rate is also factored into the channels that are scanned and discarded for the purpose of completing the scan list. "
It seems that if you scanned "backwards" the max sampling rate would be something 32 times less than the max rate.
Brad