I've installed Reftagger both with the plugin and with manual code on my wordpress.org site (at separate times, not together). I have two lists http://biblesymbol.com/parables-list/ , http://biblesymbol.com/symbols/symbols-list/ (with "Inline Google Spreadsheet Viewer" plugin) that have references in them, one is a list of parables, the other is a list of Symbols, that both have the references in them.
The plugin works just fine and the way I want it to, except that I can't customize the colors etc. for my site. It tags all the references in the list if I list by 10 per page or by 100 per page. I can go to the next set of 10 and the references are all tagged. But them I decided that in order to customize reftagger I would install regtagger manually. Reftagger then worked only for the first displayed set of references that show up as in the first 10 items, if I switched to 100 items per page then only the first 10 were tagged and not the rest, until the page was refreshed, which reset the viewer back to the default 10 items per page. After installing the code manually my site had a warning message above the plugins page after deactivating the plugin and installing the code that said something like "the code was not loaded on the back end but on the front end (or vise versa) but it would still work.
It seems like I have a choice to either have customized colors and fonts, or not have all the references tagged.
Any Ideas or workarounds?