If a part is re-categorized in the unofficial library (because a re-categorization is pending but not approved) then Bricksmith will put the part into multiple categories. If the categorization includes aliases, this makes the part inaccessible without searching aliases.
As an example, in the 14-2 part update, 4073 is the primary "plate 1x1 round" and 6141 is the alias. In the unofficial library, 6141 is the official part and 4073 is the alias.
Bricksmith's part loader simply dumps every part into every category it finds every time it loads it.
Since both the official and unofficial libraries are fully categorized, the result is 4073 going into the "alias" bucket (when the unofficial lib is loaded) and 6141 going into the "alias" bucket (when the official lib is loaded). The result is that both are in category alias, and thus neither are revealed in an all parts search without explicitly picking the alias category.
The 'right' thing to do (I think) is to suppress cataloging of the part that will be ignored on load anyway based on the load priority of the two libs.
What I do not know yet is which is higher priority (official or unofficial).