I found a new problem that I think is twist on a previous one with Deity Feats.
I created a new build that started off with 2 Rogue levels and then switched to Paladin at level 3 for the remaining levels. I selected the Deity Feats along with the other feats and saved the file. I then closed the file, but when I reopened the Rogue-Paladin build, the Deity Feats are not shown. They are saved in the build file, but not displayed. If I save the file again while the Deity Feats are not shown, the feats disappear from the saved file.
If I create a new build with Paladin starting at level 1, I can choose the Deity Feats, save, close the build and reopen it and they display fine.
I also tested a Rogue 2 Cleric 18, starting with Rogue 2, but it has the same problem as the Rogue-Paladin.
So, initially, it looks like there's a problem with the Deity Feats when they're started later than Character Level 1.
It may be that the Builder is looking at the Deity Feats to start from Character Level 1 when it should be looking from Class Level 1, if you get what I mean.