"The main problem" is perhaps the wrong way of looking at it. If all these Access databases and Excel spreadsheets became business critical then perhaps he was doing entirely the right thing!
Going the corporate 'full IT' way with these things can be very difficult and challenging, especially without first having proof of concept or working model. Irrespective of whether the model owner and IT bods are in agreement, there's always at least one, or more layers of management level funding decisions to be made in-between.