Your company has 3 sites, each with a dedicated border router, R1, R2 and R3.
Site-1 (R1) and Site-2 (R2) have their own internet uplinks, but Site-3 (R3) connects to internet via R2. A GRE tunnel is built between R2 and R3 and applied an MTU of 1440, due to some constraints in the transit network between them. You notice that traffic between same pair of devices works for TCP 1001 but fails for TCP 1002. What's wrong ?