As for the auto-pause settings, I did a bit of investigation...
By picking the options one by one, I noticed that the 'Auto Pause State' setting in baldur.ini is a decimal representation of a binary number with each autopause toggle option representing a binary digit. Here's the settings and their values on the Windows install:
Setting Value Toggle Toggle Value Setting
Character Hit 4 0 0 8 Character Injured
Character Death 16 0 0 2 Character Attacked
Weapon Unusable 1 0 0 32 Target Destroyed
End of Round 64 0 0 128 Enemy Sighted
Spell Cast 512 0 0 1024 Trap Found
Note that here there is no representation of 256 which I assume must have been assigned to a setting that was cancelled before launch.
With some trial and error I found that this setting did not translate one-to-one on my GemRB install. The crucial difference was the 'Trap Found' setting which in GemRB had the value 256 and not 1024 as in the original game. Thus my PC setting value of 1209 was meaningless here (the correct equivalent being 441). With some more trial-and-error I found that manually setting the Autopause value in gem-baldur.ini (knowing how to do it right now) translated correctly to what I could see in the settings in-game. It also works the other way around. Deleting gem-baldur.ini and setting the desired value in baldur.ini made GemRB import the baldur.ini value into a new gem-baldur-ini after which it seemed to ignore baldur.ini (confirmed by the log file).
Regardless of all these settings, how and why and where they were, nothing changed about the game behavior. For all I can see in-game the 'Auto pause state' setting is 0: Nothing makes the game autopause. I have tried with a saved game and with a fresh game. In both cases no auto pause.
I don't suppose that the value coding issue mentioned above could have anything to do with it?
Not true, actually. Starting from a clean slate (manually setting 'Autopause state' to 0 in baldur.inin and deleting gem-baldur.ini), then setting all autopause options to on in-game revealed that 'On hit', 'When attacked' and 'End of round' fired as they were supposed to. 'Enemy sighted' and 'Target destroyed' (and possibly 'Character Injured') was confirmed not to.