The issue we were seeing appeared to effect all our wab apps (custom and built-in) and portal web maps when embedded in iFrames. However, the issue only appeared in Chrome and it was domain specific. We have one server that sits in a dz and accepts requests from the public internet. The other is only available internally. I created a quick test app and placed iFrames in each that pointed at a portal app. The popups showed on the internal box but not in the dz server. The popups were working in Chrome before the recent updates Google posted.
Our Portal is running at version 10.7.1. The layers with the popups are map services.
I have Google Chrome on a personal machine that is running the same version as my organization. The popups worked with WAB 2.13 on my personal machine. I tried reverting my chrome version on my company machine and that worked until a nightly routine pushed me back to 89.x. ESRI reported that they are getting a lot of calls in regards to chrome and they believe it has something to do with user profiles not being setup correctly. The resolution we found involved updating our local wab app to version 2.19. I understand that isn't really an option for larger orgs with many apps, so maybe you should start a case with ESRI.