It happens to me too, same simptoms, I see it mostly on cyvr, bu again it happens on all other airports by fsdt and flightbeam that I have, not always but it does, where a part of the terminal or a complete building won't appear. They reappear if I move closer to them. So you are clearly not the only one. I just learned to live with it :-)
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Do you know the system specifications for your PC? It could help this problem.
Two other things when restarting couatl while reading my task manager the "Disk" jumps to 100% when loading or restarting couatl could this contribute to the problem? GPU temp's also stay at around 65'C when restarting. I also read that the shader's for the 8400HD version ins 5.0, is it any good?
I'm currenty still considering a new graphics card, but its a risk because it might not fix the problem. It could also bottleneck my PC at the same time making it almost no faster than my old GPU therefore a waste of $200-300.
There was also a time when I reinstalled addon manager's latest update but for some reason couatl(lets say 1) didn't close so there where two open couatl 1 and couatl 2. When restarting couatl, the buildings from couatl 2 stayed on(couatl 1 buildings dissapeared) but there was only a small pack of buildings and coincidentally it was the missing buildings without help from the 2nd couatl it wouldn't have displayed. There was no conflicting buildings, or textures, (just the missing buildings) and performance didn't decrease or increase.. There is no way I could recreate this situation but two coualt engines running seemed to have fixed it somehow.