The route requires the US Loco and Asset pack to be installed and it wasn't so as soon as I installed it the tunnels are fine! Looking on the JT website this is listed as a requirement so I perhaps should have seen that but it isn't mentioned in the manual or on Steam Store. So anyone else who has the tunnel issue, check you have the US pack installed.
Thanks everyone for your help, particularly gptech for sorting the route markers and GWR HST
