Ok, that at least proves the problem doesn't have anything to do with CYVR, but it's another scenery you have in conflict. The small .BGL should have fixed the issue of the different behavior when starting a flight or arriving there, but if that hasn't fixed it, it means the conflict is caused by another scenery.
Most likely an AFCAD for the same area, possibly even not strictly related to CYVR, there are some free scenery of the embedded seaplane base, for example, that should be removed.