I just tested it, and my left and right CTRL can be mapped and used indecently. I tested this using MAME. I am using one of the newer IPAC 4 units that just came out about a couple years ago.
Also, if this is your "default" layout, I'd advise against using keys like CTRL, SHIFT, ALT and such. Those keys activate Windows shortcuts, and can lead to trouble.
Although, if it's a custom layout for some game that can't be changed, then ignore my above rambling.