Now that there are several new AFCAD files available for FS2004 I decided to try some of my older simflyers scenery, but there is terrible flashing of the ground textures with the base textures showing through the aprons/taxiways etc. Is there any fix for this? Or is is just something you have to live with?

There is an upgrade for FS 2004 Simflyers sceneries.

Well I have applied the updates that are for gates disappearing but the other update only allows you to install the sceneries in FS2004. They don't fix the texture flashing. At least it doesn't claim to do this and I haven't read about it doing so in their forums.