Is it possible there are more ships available at the era you're using than OP can show? I believe the limit was increased to 128 per size class (DN, CA, CL, FF, F, SB, BATS, BS) with 2.5.3.8. Are you using the latest patch? If not, you will definitely run into problems considering the sheer number of ships FS added. If you're on the right patch and the ship numbers are under the limit, have you checked the shiplist to see if any restricted availability tags (R, SPECIAL) are used? Have you checked the availability dates?
I'm just throwing ideas at the wall to see if anything sticks. If none of the above help, maybe FS can shed some light.