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What is the priority of your thread? try to see which thread is grabbing the processor after your interrupt and you need to set priority of your thread higher than this. Offcourse you have to be carefull not to get too swaped in this thread and hang other main threads like the network thread.
Another Idea is to split your work, do only the urgent part in the IRQ handler (should be short though), and defer what can be delayed to a later no time critical thread.