The Many Potential Variables of Dysfunction
By incorporating the Seeker into a RW project we are inserting a potentially troublesome mix of jQuery, CSS and HTML into a theme most likely designed around its own delicate balance of well-crafted code.
So it is important to remember that we, The Seeker, are the guest rather than the host. We must proceed a step at a time, and always be prepared to take several steps back if something breaks or doesn't work as expected. Workshops are a hands-on learning experience and boundless patience is an essential prerequisite.
It is possible that your theme already has jQuery built in, as is often the case now with the more recent themes. Even though we've included a No-Conflict call in the code, this may still result in unforseen conflicts. But unforseen does not mean insurmount-able. More recent themes seem to work much more reliably with jQuery.
For those of you who are more advanced and working on larger, more complicated sites, it may well be a better idea to hardcode the jQuery into the index.html file. If you want to see how this is done, take a look at the RapidWeaver Central source code.