You don't say which flight sim you are using.
If you are using FS9, this has been discussed already: when a scenery has custom hold short markings, the default should be removed, but FS9 doesn't allow this in a clean way, but requires to either set the taxiway width at 1 ft, or to modify the ground textures around the hold short zones, in order to conceal the default one, without really removing them. This might create such issues in FS9, but it's not so automatic: it also depends on the traffic density and models used.
In FSX, there's a proper way to create an invisible hold short markers so, the problem doens't happen. As everybody probably knows by now, we design the scenery in FSX, and we don't do much testing under FS9. So, you shouldn't have this problem in FSX, I hope.
However, it's strange you say all sceneries have this, except KFLL and KJFK, since most of this discussion happened just for KFLL, which lead to a subsequent fix. So, it's quite unusual that we had lots of reports for KFLL, which was the last scenery we released, but not much for the other sceneries that have around for much longer.