Certain Custom Fields (CF), whether they be user-created or system generated (i.e. Resolution is one that is impacted by the this issue), are not visible/do not show up in the list of CFs in any of the Field Configuration Schemes for projects.
However, I have re-named of one of the CFs and it has now appeared in the Field Configuration Scheme for the project.
This is not a situation where CFs are not being displayed, this is a situation where CFs, that can be seen/edited via the Custom Fields section under Administration, are not showing up in Field Configuration Schemes.
Also, a full re-index was performed.