It sounds to me that you haven't perfectly lit the caves. Plus, you need to make sure you've lit up at least 128 blocks from the largest area you will be in. Any unlit caves within that range will slowly fill with mobs until the mob cap is reached, and your farm will be useless.
Related to your computer/render distance: if you spawn mobs in caves while in the minecart, and the chunks are unloaded due to your render distance when you move to the other end, they may stay alive and slowly build up until they reach the mob cap. This could be possible at render distance 8 or less.
Explanation about mobs not despawning outside of the 32 block radius:
From the wiki: "A mob that has had no player within 32 blocks of it for more than 30 seconds has a 1 in 800 chance of despawning on each game tick (1/20th of a second). Therefore, the half-life of monsters not within 32 blocks of a player is 27.73 seconds (after the initial 30 seconds have elapsed)."
This means that it takes an average of nearly a minute for a mob to despawn once it is outside that range. With your minecart, many mobs would never despawn, and again, if your chunks get unloaded as soon as (or even before) you get 128 blocks away (render distnace 8 or less), the mobs won't despawn even then.
Advice:
Make your radius extend beyond 128 blocks from the furthest extent you might go to at the farm. I've done a 150 block radius at my witch farm - 150 blocks from each side of the witch hut. Make sure you have properly lit every cave inside that radius, i.e. light level 8 or above on each spawnable block. If there is even one unlit cave, that's hundreds or thousands of spawning spaces, and mobs will spawn quite a bit faster than they despawn.
Addendum:
Another thing to check would be slime chunks. Slimes do despawn now, but at the same rate as other mobs, so even when you have the caves lit, if you want perfect rates, you'd need to slab or fill in any slime chunks. You can use a slime chunk finder online to locate the slime chunks in your region.
Is that half block under those red crosses? If so, half block does not work for spawning. Quick search only, try this link: http://www.minecraftforum.net/forums/archive/alpha/alpha-survival-single-player/820173-mob-spawning-science?page=1
If that is a full block, follow the answer from @TrueDakkon and add a space above and beside the red crosses. (Sample: Move the top part at least 1 block then add another block on the side of those crosses. You will now have 3 wide 3 height. Try it from there)
P.S. I don't have setup now and I cannot verify my answer. I will try to verify as soon as I got my hands on a Skyfactory setup.
Best Answer
Because there is more water outside of your farm then inside, more squids spawn outside of the bounds of your farm then inside it. You need to remove all the water outside of your farm to a distance of
128 blocksfrom your player(the distance at which mobs stop spawning). You also need to make sure that when you use your farm that you stand at least25 blocksaway from your farm, for that is the distance at which mobs start spawning.Remember, if mobs are spawning outside your farm, they are therefore not spawning inside your farm.