E6 FD doesn't fail at once, it slowly loses activity over time. If you get the impression, that your slides look a tad darker than they should look, you can try to extend FD times. Only if that doesn't give you the results you want, then it's time to start with a new bottle of fresh concentrate. Your statement 'the final film rolls are not as transparent as' tells me you should either extend E6 FD times by 30-60 seconds, or replace E6 FD.
The discoloration of E6 CD after use is normal. There is a competitive coupler in E6 CD, which forms a colorful but water soluble product with oxidized color developer. This colorful product will eventually react with Sulfite to form something mostly colorless, that's when you see E6 CD regaining its original appearance.