Is the issue partly connected to aircrew familiarity? Loganair crews will be very familiar with the procedures and potential issues at Dundee as they are based there and/or regularly fly there. Flybe crews are presumably drawn from a large pool so they will have less opportunity to achieve similar levels of familiarity.
With Leuchars no longer operating as an air defence station, is radar guidance from them still normally available for aircraft approaching Dundee?