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Yes, the MSS option in the SYN and SYN/ACK are advertisements and not a negotiation. When the adjusting of the MSS value is different for each direction, this could lead to problems in the same way as when no adjustment has been done.
If you have control over the devices that to the adjustments, then you can fix it there. If not, you might want to change the MTU on one of the endpoints or make another intermediate device under your control adjust the MSS to the lowest value.
