Hi

I think that when you enable the module, it does not gather the terms added in periods where it was disabled.

Example:
termA
termB
-->install module (It inserts termA & termB in search_index)
termC (inserted too)
--> disable module
termD
--> enable module (termD is not inserted in search_index)
termE (inserted)

I think that the query of the update_index should be modified to get all the taxonomy seach terms with null created or changed, but i haven't tested

  $result = db_query_range("SELECT td.tid, th.changed, v.name AS vocabulary_name
                      FROM {term_data} td
                        LEFT JOIN {vocabulary} v ON td.vid = v.vid 
                        LEFT JOIN {taxonomy_search} th ON td.tid = th.tid
                      WHERE (th.changed = %d AND td.tid > %d) OR (th.changed > %d)
<b>OR (th.changed IS NULL)</b>
                      ORDER BY th.changed ASC, td.tid ASC",

Thanks for the module btw!