Could it be that 1) you do not produce anything they need/lack at the time; 2) their trade routes are blocked?Trade:
Countries you trade with (have negotiated a trade agreement with, as shown in the diplomacy window) do not appear on your trade list. Neither is any income from these countries.
I had this with Sweden when playing UK campaign and with the Ottomans when playing as Prussia.
I usually see everyone I have agreements with in my list though.
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