7i96 Configuration Tool

Can they be modified with the tool? Should have "inverted" or "invert" besides every IO pin.

No, not in John's tool, unless he's changed it in the last couple of weeks. Hence asking.

Upload the hal file, please.

Here they are

There are no inputs or outputs set up in the attached hal file.

Thats what I concluded, but that is the hal file that John's tool generated and the switches are definately working, just the inverse of what I want. Could it be more than one hal file is produced and they are in another one?

Did you look in the ini file, inputs and outputs seem to get a mention in there.