The latest patch does seem to have corrected the problem.
I am having a similar problem, I have always had custom Super Bland Eyes from Mod the Sims, but they always worked without a hitch before. A female child Sim's eyes change color when switching sims in CAS.
Did you make sure that the custom content still works with the newest patch ? This could be a cc issue.
2 patches already, and male eyes still not fixed.
If the user above is using eye replacements that are tagged with the proper EA eye tags, that would explain why their CC eyes don't work, since the original eyes the CC ones meant to be replacing aren't working either. Someone said that the broken 5-6 male eye colours have simply been untagged from males, similar to how March patch also made teen girls lose some clothing and half the heels (which has been fixed since).
The "broken" eye colours are:
Swampy green, 6th from left, top row - changes to bright green
Grey green, 1st from right, top row - changes to bright green
Dark grey, 5th from left, bottom row - changes to light grey
Grey brown, 3rd from right, bottom row - changes to brown
Purple, 1st from right, bottom row - changes to red
