I also have an application using SCXI and DO's with the AI-16XE. The SCXI requires the use of 4 of your DIO's for multiplexing. To check which ones are reserved, look in MAX utility at the Test Panel for the AI-16XE. The Digital I/O tab will show the reserved lines as greyed out. The other lines are available for your use, but you must use a Digital I/O VI that only deals with the available lines, and not the entire port. I use the 'Digital Group Config.vi', 'Digital Single Write.vi', and the 'DIO Clear.vi' along with virtual channels for the lines available for my use (personally, I find it simpler with virtual channels, but I'm sure it will be fine without). I would send an example, but my application is embedded in a complex program. After the proper analog and
digital configurations, the analog read and digital write vi's can run simultaneously.
You probably have already noticed, but you must also tap off of the 50 pin connector on the back of your SCXI inorder to access your DO's while using the SCXI.