Is it possible for the search box (upper right of the web interface) to search through custom vocabularies?

Essentially, if you have a vocabulary with 'foo' and 'bar', for example, searching for either of those in the top search box won't turn up any documents that have that vocabulary term applied to them, in the case of our custom vocabularies.

Is there any way to make this (vocabulary term indexing) possible?

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This works for me. For instance I change a document to have coverage of "Europe / France" then searching for "france" in the top search box returns my document. Can you give specific examples of what doesn't work? Are you using the vocabulary id or the label in the search (just the label won't work, but can be made to with a bit of code).

Say, in the "virtual navigation", you have a group, and that uses a custom vocabulary to tag documents. The possible options for this vocabulary are 'foo' and 'bar'. If I search for the name in the virtnav, the search won't return the documents that have that tag. I should notify that the given attribute is not a native/vanilla one.