Hi,
All keywords go to the same exact table, including the custom fields. One thing to note with partial matches is, that by using the index table engine, mid-word matches are not possible (indexed queries does not allow that in SQL). So if these items are in the index table, and indeed the index table is used, then they will match – regardless of the source. This might be more likely a configuration related issue.
May I ask how many rows does the index table have roughly?
When the index table is enabled, the custom field selection per search instance is not possible, that is on purpose. The index table is a very simple concept, is has to be – to store the least amount of data possible.
Therefore after indexing, there is no way to tell which custom field the keywords are originating from – therefore it can be only configured on the index table panel.
The highlighter should work on whatever field on the live results list. It is not running on the server side – it is executed via javascript after the search query is processed.