This was originally discussed in https://community.logos.com/forums/p/117418/771430.aspx#771430 and following.
Veli - who flagged the issue - posted the screenshot below - which shows the NA28 critical apparatus appears when running a Guide on John 3:1-15 but not John 3:1-5 even though there is an entry for verse 3.

I can't reproduce this on 6.6 SR1 or 6.7 beta 2 (I get results in either case)
Thoughts appreciated, Graham