For those that might be having problems with analog inputs when
using WPIlib (C++) on the cRIO, an update was posted at
http://first.wpi.edu/FRC/frcupdates.html
that is reputed to address this problem, amongst other things.
There is a caution to keep a copy of the prior update around in
case there are unexpected issues with the new update.
Toothlessness of locking for semaphores protecting the
registers used to access the analog inputs led to problems with the
battery voltage showing up when other analog inputs were read.
If you are using analog inputs to control things you should have
a look at this update of WPIlib.
Eugene