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Commercial jets are pressurized to 8,000ft elevation. This reduced cabin pressure causes all kinds of funky things to your body and especially joints. If you have preexisting body aches, arthritis, past injuries, inflammatory conditions or other auto-immune diseases it's quite possibly exacerbating an underlying condition.
As others said, talk to a doctor or two.
^^This^^ The joint pain is definitely inflammation during cabin pressurization, but if it is severe enough it could also impact the brains circulation and lead to an aneurysm.