I am not sure if this is a bug or working as intended, but it seems off and is different than the last time I used the Domain Changer.

I made a new cleric and needed to take one of the Amia specific domains instead of a default (Fate).

So I clicked the domain changer, got the dialog asking which domain to change.

I chose: Protection to Fate

I got this message:
0 - 0
Kelemvor 36 41 44 15 48 18

Then nothing else happened. I still had Protection listed under feats so I relogged. Nothing changed. I went through the process again, and it worked.
0 - 0
Kelemvor 36 41 44 15 48 18
Changing your domain from: Protection to Fate
You will be booted in 5 seconds so that the old domain feats can be removed.
Verified that your domain feats were added.

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Iim'mur'ss - Grandmaster Shadowdancer / Aaralyn - Diplomat / Oleander - Toxic Desert Flower

This sounds like a stray variable was left on your PC from something else.