Supressed Assembly Features show up Unsuppressed in Part

Hi,

I've run into a problem that the assembly features behave different in Assembly than in Part. As shown below "Cut-Extrude 8" is unsuppressed, but the 3 Assembly Features at the bottom (starting with "gaatjes"). This is an issue because we 'scroll' through different configurations of the assembly and once unsuppressed in the assembly they remain unsuppressed in the part even other configurations.

Another problem is that after a hard full rebuild (ctrl-shift-Q) all features (holes) show up instead all being suppressed.

This problem is because of propagate feature to part, but this is necessary because the files will be laser cut and otherwise the features won't show up in the laser file, so turning this off is not an option.

Does anybody know how to manage this properly? 

Thanks