Thanks for your answer. I tried another approach in the meanwhile: creating a custom template (Custom Modx theme) which I use to inject some custom css to fix the z-index.
@markh Maybe this could be a useful fix to be included in one of the coming modx releases, as I can imagine that also other users may face this issue.
This is the CSS that I used to fix the alignment of the modal windows:
#contentblocks-modal-mask {
z-index: 251!important;
}
#contentblocks-modal {
z-index: 252!important;
}
Other values for the z-index may of course also work. Seems to be working until now.