I haven't worked with Shimadzu FTIRs, but with a number of other types.
First, can you be more specific about the problems you are having with moisture?
Typically, the problem is with the moisture causing a LOT of background noise in
the spectrum. One way around this is to make a larger number of runs, both for
your background spectrum and your sample.
But, sometimes the problem is much worse. For this reason, most manufacturers
include dessicants in the sensitive areas of the instrument. It could be as simple
a problem as bad dessicant.