Sorry @Jip, this took a while but I have an update on the isse (game log and video link attached). Note that this time I did not use any (Ui) mods whatsoever:
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The factory queue stops being responsive if there is a longer period of no factory queue updates, i.e. no units roll off or no unit is added to the queue
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This apparently is not tied to a specific factory but rather to any factory in the game
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The issue is easiest to reproduce if you stall mass, i.e. units roll off very slowly and factory queues are therefore not updated and no units are added to any factory by the player.
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Therefore, this issue should be reproduceable already in early game, which I managed to do after about 8 minutes in a separate game (not in video). Just build a bunch of factories, que in a bunch of different units, stall really hard and try to drag & drop or right click in any factory queue. If queue is not responsive, either add a new unit to a queue or wait for a unit to roll off the factory. This should allow drag & drop / right-clicking again.
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My best guess is that it has to do with how factory queues are handled / polled / updated within the game mechanics
Game Log:
game_21399981.log
Video link:
https://youtu.be/ht7IDmaB1KI