sometimes if you have something selecting before exporting, only this one thing will be exported.
For example, it is common to have a 2D tracks selected without knowing and when exporting into the 3D app, only this track will have been exported.
In your case, since you have two groups, make sure that none of hte two are selected. You probably exported when the 'background markers' group was selected.
Otherwise, all markers should export nicely.