There may indeed be an issue when read marking is changed that way. Probably this will resolve itself over time, can't think of anything I could do to change that.
Anyway, there seems to be another issue (also one I can do nothing about): there might be a read marking problem if there are more than one page of new discussion entries. I have now had members of my board experience this for the first time, and due to increased traffic in groups (because of the notifications

) they had more than one page of new entries. Read marking seems to hickup then. This not only was influencing my mod, but also read marking on the main groups page (my groups). The discussion was indeed marked read, but the group was not - systemwide, not only for the notifications. I also was able to reproduce this, albeit both was on 3.8 installations. Since there were no changes to the system, I'm pretty sure this will be true for vB4, too.
Anyway, to resolve this if it happens, my users had to use the groups->individual group page->group tools->mark this group read. This worked. Going throug unread discussions or marking individual discussions read will not, since read marking for discussions and groups runs seperately.