I guess my next question then is could a custom hook and snippet be written to deal with making sure the checkboxes stay checked? I'm presuming "yes", but not sure how to proceed on this?
Of course the answer is yes.
If one knows php it could probably be done faster than figuring out why FormIt is not working!
How to proceed depends on what you are trying to do - in more detail than "I'm trying to keep a check box checked".
Detail would be: when validation fails, or when ...
Detail would be: the checkboxes are an array of values... (I say this because if you give each check box its own name FormIt can keep them checked, it only seems to have problems with arrays of checkboxes - so calling them test1, test2, etc works, calling them all test[] fails) If you can deal with them having separate names you could use FormIt.