Are there any other rotation/positioning/scale problems with the code I posted? It all looked the same as the plain LoadAnimMesh() to me. The -90 thing seems a bit ugly but I think it may be the best you're going to get.
Also, try commenting out that block of code and replace it with:
RotateEntity Obj\ObjHandle, EntityPitch#(Obj\ObjHandle, True), EntityYaw#(Obj\ObjHandle, True), EntityRoll#(Obj\ObjHandle, True)
In theory that should do nothing. If it turns your objects there's a problem.
Also, try commenting out that block of code and replace it with:
RotateEntity Obj\ObjHandle, EntityPitch#(Obj\ObjHandle, True), EntityYaw#(Obj\ObjHandle, True), EntityRoll#(Obj\ObjHandle, True)
In theory that should do nothing. If it turns your objects there's a problem.