Which port, i will assume port 1 and that it is enabled.
Are you duplicating pins by some chance as those are often used for the motors, don't need to.....
You can use the Automated Setup Of inputs dialog, i have never used it, but may be worth a try.
A long while ago, with one of the versions ( don't remember which version), i had a problem with Mach not accepting the input values and it took a number of times for it to save them. I just wrote it off as a fluke!
What version are you using?
Post your xml file and the pins you want assigned and we can take a look.
RICH