Pilotage - not wishing to sound insulting, but I had a similar thing (warning me of danger zones over Iraq for a flight from Perth (Scotland!!) to Edinburgh). Reported it to Mike Cross who very helpfully pointed out that I'd left the IFR / VFR selection at the default, rather than selecting VFR
Just a thought...!!
PS I'm about to go check NOTAMs myself for a trip from Perth to Benbecula tomorrow, so will be able to let you know if I concur with your issues!!