This was reported recently, and I did put it down to the Prepar3d v4.4 scenery display bug which was fixed in 4.5, but the guy who had the issue updated and it still didn't work. So I'm sorry this has taken so long to acknowledge, but I'm never been able to replicate the issue.
Following the issue with NZCH's flashing ground polys, these were tracked down to the custom runway at West Melton, which I promptly removed from the release version. Which ended up as a bit of a nightmare, but I'll cover that separately...
It may be that this is a similar issue with Dunedin. A discussion over at AVSIM has just had a post which certainly points to this, as he was able to fix the issue by disabling the ground polys at Taieri. This isn't a long-term solution, as Taieri is my favourite airfield, so I will see if I can track down a cause, and release a patch for Dunedin if possible. This will take a few weeks, as I have some tedious family commitments for a week or two.
This issue seems to be new in later releases of Prepar3d v4, but I'm not sure if it is something which LM may see as fixable.