you got opacity other than "100%" or blend modes other than "Normal" in one of the objects. change it to the default and try again.
changing the opacity or blend mode other than the default to any object in your illustrator file will cause the "create shapes from vector layer" to behave in the following manner: your shape layer will have an additional group in the shape hierarchy that will contain paths and merge operation that constitute a transparent Ai artboard. it's very annoying.
it could look like something like this if you work in an HD Preset.
BTW HD preset gives you 2 artboards.. it's actually a good thing:Re: AI (illustrator) layers not showing up in AE (after effects) CC 2014 )
here is the shape hierarchy comparison of Layer 1 that is normal and Layer 2 that has 50% opacity:
as you can see the artboard is here as a group with 3 paths and there is an additional merge path operation to the content of the shape.
What to do?
- if it's after the fact: you can just manually delete the group and the merge path from your shapes, or remove the blend mode / opacity from the layers in Ai (or set them to 100%/set them to normal) which is what Ae is going to do anyway, save the file again, and create shapes from vector layer again.
- before the fact - proper workflow: it is already known that opacity and blend mode (and not only them) don't translate to a corresponding shape anyway, so this makes this an easy workflow decision: if you do plan to convert to shapes, prior to importing to Ae - set your blend modes to normal and opacity to 100% in Ai if it's not.
- there's also this script: Explode Shape Layers 3 - aescripts + aeplugins - aescripts.com that is very handy for dealing with the whole conversion of Ai to shapes and it has the "Remove Artboard" feature. this from the script description: If any of your Illustrator layers have non-100% opacity or go outside of the frame, you've probably noticed that converting brings in an empty artboard artifact that gets in the way. No more! Remove it with Remove Artboard.
One last thing:
the only reason to ever use the "create shapes from vector layers" feature is if you are planning to manipulate the actual path of the shapes, or use any of the shape operators (repeater for example) or maybe extrude them through the C4D renderer. that's basically it. shape layers are complicated. they are always continuously rasterized and each path of your illustrator artwork will get it's own shape group hierarchy - it's get's messy very fast. so if you are not planning to do that, you should just let them be pixel layers. if you need vector functionality, you can press the continuously rasterize switch.
Thanks so much for the thorough explanation. That was the problem. I didn't even think to check that. I checked everything else under the sun though. It makes sense. Ok, let me go share the good news.
You're welcome Jeremy. this issue is troubling users from time to time and the information is here in the forums if you are looking hard enough, help others find this quickly by marking the response as correct.