Interaction between Field Group, Field Collection, and the Theme Layer

I'll start off by saying this may not be a Field Group bug. However, I figured this was a most excellent place to start.

We have a site with a fairly complicated workflow, where a number of user groups will be accessing the same content and exposing additional fields / components (based on progress and user roles). We have accomplished this by nesting field collections inside of field groups.

All is well on the form, and all is well for 1 of our 3 field groups on the node view page. HOWEVER the remaining 2 groups absolutely refuse to display their content.

I have tried moving the field collection out of the field group on the display page, and it suddenly renders fine.

I have tried creating different field groups, different kinds of field groups, etc. and nothing.

I have tried debugging through the various functions in the field group module, and throughout most of it I am able to see that these groups DO have children. However, when the data is finally presented in the $content variable in my theme (an Omega sub-theme) 2/3 of the groups are simply empty.

I know there is data there, it shows up in the form and in the database. I just spent a couple of hours writing a theme function that manually goes and finds the fields that should be in the groups and renders them, however this isn't a sustainable solution (and is so specific to this site that it won't address the bug for my other sites or anyone else).

Does anyone have any thoughts here?

We ARE running field permissions, and I have verified that the group that works and the 2 that don't have the same permissions. I've tried updating to the most recent field group dev, and no luck. Field Collection is already up to date.

Thanks much!