Do you have multiple defaults at the same time? You can only have one set of default replacement eyes at a time, since they replace the in game eyes, it doesn't add on any colours, so if you have multiple default replacement eyes, you're telling the game to replace the normal eyes with loads of different eyes and.. That doesn't work.
But, you can have multiple non default eyes which do not replace the in game eyes and simply add on to the number of eye colours in the eye colour menu. You can also use eyes under the facepaint category too if you want extra swatches, sims won't inherit them genetically though, it counts as makeup so you have to apply it to each outfit if you're using facepaint.
Edit: reread your post oops um do check the default replacement thing but the thing with the toddlers is probably because that set of default eyes hasn't been updated for the toddlers patch, perhaps?