Oh that's actually because the lazybones transformations use its own set of eyes in its files. You can change this with some editing though, but you'd have to do this for every transformation file (the lazybone ones, the .x2m's).
You're gonna need Eternity's mod tools for the skill creator and costume creator. It's part of the mod installer tools.

1. First of all, you can open the .x2m file for the transformation with a program like winrar to find the costume file attached to the transformation (this is what changes your character appearance). Extract it so you can edit it in the costume creator tool.

2. Open the costume in the costume creator and tab over to the race you're trying to edit but you should do this for both genders if it's a saiyan/human. The different entries in the drop-down button are for the different levels of transformations. Go to the entry that has stuff in it. Now, something to note about these files, the one that says "face_forehead" helps dictate the SHAPE of your eyes and the one that says "face_eyes" are for the pupil of your eyes. I'm assuming your talking about the shape itself so main one here to worry about is the forehead one.

3. You have some options at this point. You can change the number the files are pointing to to a custom eye file that you have by changing thr number to the number of the custom file (looks like HUM_XXX, or the mod might have it somewhere in a text file). This would make the transformation have that set of eyes BUT only that set of eyes for every character. IF you want the eye shape to stay the same for your CAC when you transform, then you should: replace/delete the face_forehead text and the face_eye text to make it the same as the other sections that say <---this directory is empty---> or something like that. Do this for both gender tabs and for every entry you want to edit. Once you're done, you can edit the name of the costume file in the file tab to make it easier to identify. Save it somewhere when you're done cause we need it.

4. Open the transformation skill in the skill creator and go to the last tab BCS. Where it says costume or whatever, click remove and then click set. Find the costume file you just made and select it and remember to click EMBEDD, not link. Once that's done, save the skill file somewhere, with a different name or something.

5. Install it like any mod file and it should work now. The eyes should now stay the same for the character when you transform.