When you enable white-listing, you are effectively saying: “I know better than Kodi and the Adjust Refresh Rate option (which also switches resolution), or I know what I’m doing”. You are overriding the choices we would normally make on your behalf during playback.
Did you whitelist the 3D modes? 3D modes can now be configured manually in the whitelist I believe (CC @tanio99).
If you didn’t, it’s not a surprise that you don’t get put in to a 3D mode.
I am not sure why you need a whitelist – unless you have specific reasons. Otherwise you should have an empty whitelist and Adjust Refresh Rate enabled.
Whitelist means only allow these modes. If you omit some, we won’t switch to them, because we assume that you made a conscious decision to prohibit them.