I've found the issue. Short story ensues...
I was on the testing team when NWEV3 was being built. I left the MSTS scene before the building and testing of V3 had been completed. Apparently I also didn't think to download the public download version of the route when I came back on the scene!
The activities, as I said in my last post, should still run as intended after clicking through the errors, I don't think much in the way of track and interactives changed in the 3 or 4 months between me leaving the scene and the route being uploaded. From memory, all that was left was a little bit of scenery placement and a couple of others' activities were needing finished.
I am in the process of downloading the route, once that's done it should just be a case of re-saving all the acts, re-packaging, and re-uploading. Nothing will've changed except my version of the route will no longer be a massively outdated testing copy.
Sorry for the mix up, all be sorted soon enough.