Confirming the same bug. It appears that checking the taxonomy on the media edit screen adds a acf-hidden class to the meta box. The screenshots linked below show the meta box class before and after checking the taxonomy item. The other screenshots show the ACF field group settings.
WordPress Version 3.6
ACF Version 4.2.2
No ACF Add-Ons.
No other plugins.
Chrome (OSX) Version 29.0.1547.57
Before taxonomy checked:
http://cl.ly/image/3v0X2k2D0m1e
After taxonomy checked:
http://cl.ly/image/3z2b3f1r2c2Y
Field group settings:
http://cl.ly/image/1b450G2Y2l30
http://cl.ly/image/2J0K0Y1I352o
