The chooser that is displayed when the user chooses to prepare a spell with metamagic feats applied cannot choose between different versions of the same feat that are selected with a CHOOSE when the feat is taken.
A feat for which this issue occurs is Elemental Spell from the Pathfinder RPG Advanced Player's Guide, which can be taken multiple times for different energy forms. If a character has multiple versions of a feat like this, these cannot be individually selected when the feat is applied to a prepared spell.
See for the data part of this issue.
The new solution to the implementation of the feat in question requires a change in the behavior of the metamagic feat application chooser. Now, the chooser will no longer list Metamagic feats that are VISIBLEISPLAY. This has no adverse effect on other feats, as previous to this change there are no such feats in any PCGen dataset.
Implemented as of Subversion revision 20396.