The popups still start not showing sometimes. Although I don't yet know what triggers the start of this problem (might be the science screen, as noted by Juanholio). However, I find that opening the science screen and subsequently closing it fixes all missing popups I should have got until that moment.
Example:
0) (starting at some trigger) Popups don't appear anymore.
1) I meet a city state: no popup appears. I clear ruins: no popup appears. (Usually it takes a couple of missing popups before I realize I should have gotten one
)
2) I open the science screen and close it again.
3) I get a popup "You have met...", after that a popup "You have received culture", etc.
4) All popups work again as they should. After a while, the situation starts again at 0).
In state 0, the popup events appear to be 'saved', but their effects will only take place when the fix (2) is applied. Most notable are city capturings: without the popup the city is auto-annexed but the happiness/culture effects are
not calculated yet (the popup choice seems to trigger that effect). After step (2) the choice for annex/puppet is given and effects are calculated accordingly.
Note: after the hotfix, I haven't yet captured a city in state 0, but I did experience the described behavior (1-4) with CS/ruins post-fix and the described capturing behavior pre-fix.