Should parking counts include handicap stalls?

All automobile parking spaces should be included in your parking calculations (typical, handicapped, reserved, etc.), so it appears that you're doing the calculations correctly... Perhaps it's confusion on the wording of the review comment and the specifics of your project regarding where you've located the LEED preferred spaces? Note that your designated preferred spaces must be those closest to the entrance AFTER all of the required handicapped spaces required by code. For example, if you were building a school, the order of closeness would need to be: handicapped, LEED preferred, reserved principal/vice principal, and then general public. If you put the principal's reserved space closer to the entrance than your LEED designated spaces, those spaces then wouldn't meet the LEED definition of preferred (as there would be a non-handicap space closer) and you're receive a comment that might include working about handicapped spaces. Again - I don't know if that helps at all, but that's where I've seen a comment related to handicapped spaces appear. If the issue appears to be something else, please feel free to reply.