Some additional info:

The skycubes are declared like this:

ENTITY* cube = {
type="skycube04_high+6.tga";
layer=2;
z=5;
flags2 = SKY | CUBE;
}

ENTITY* cube_moon = {
type="skycube07_high+6.tga";
layer=2;
z=5;
flags2 = SKY | CUBE;
}

None have the SHOW flag set ... this is done separately when the levels are loaded. It's always only one of them shown.

The error occurs only if both skycubes are declared. Both work fine when standalone, but together they override some memory with the result that some engine variables are overwritten (e.g. the nexus value).