I've tried some taxi on the incriminated runway with my trusty 707-700, and then with other planes.
Indeed on the location you speak about there seems to be a unevenness of sort even on my sim, though it only made my planes nose gear dance slightly and not fall through the runway.
I think it might be worth to remedy with AFCAD, though. As under the runways usually the scenery is not flattened, it suffices to add a invisible apron's layer under the runway and everything should go smooth again.
PS
Tried adding apron layer underneath runway. No dice. Still trips. Yet is really small and that gives no real problems beside a little, less than one feet jump (at least on my system). I think I'll leave it alone.
PPS
Found the additional PHNL AFCAD I was using to be incredibly shoddy. Whoever did it and then published did one hell of a poor job.. Thanks for having, even if unwittingly, make me aware of it needing corrections.

There's but one real cure for human stupidity. It's called DEATH.
At the moment mourning the assassination of sarcasm and irony for the good of the "higher".
Proud FSIX user. Active user of FS98, X-plane and novic