Playdate SDK 1.12.2 (and I believe earlier) on Ubuntu Linux.
Take an out of date SDK (so that you'll get a notification about the newer SDK). Use it to compile a program that fails before running update(). For example:
src/main:
missing.x =1
$ /opt/PlaydateSDK-1.12.2/bin/pdc src out
$ /opt/PlaydateSDK-1.12.2/bin/PlaydateSimulator out.pdx
Expected behavior: two popups, one notifying me that the program failed, and another notifying me that 1.12.3 is available. Whichever one is on top is active.
Observed behavior: the program failure popup ("The file could not be loaded") appeared and was almost immediately covered up by the "SDK Update" popup. However, the SDK Update popup is disabled until i dismiss the program failure popup which is behind it.
It's a minor nuisance, but I seem to run into every time. (I don't permanently dismiss the popup because I want to annoyed until I get around to installing the update. I unusually delay until I've finished my immediate task. At one point I had to stick with an old release for a while because the newer SDK was available, but my physical Playdate was not offered an upgrade, and would not run the output from the newer SDK. That would probably have been 1.1.1 to 1.12.0 or 1.12.0 to 1.12.2.)