Jim,
The v5.1.0 and v5.1.1 releases had a separate setting for "Load jQuery" and "Load Bootstrap" for each of those Javascript files. Unfortunately, loading those standard files (or relying on sites to load them already) had tons of conflicts with extensions loading jQuery or the Bootstrap Javascript multiple times, which causes conflicts with some features.
In v5.1.2, we moved to a new compatibility layer. The "Load jQuery" setting now loads a combined jQuery and Bootstrap Javascript file which is meant only for JFBConnect and the SCLogin module. That shields it from other conflicts that may be on your site. If disabled, then you should have jQuery and Bootstrap loading on your site already and JFBConnect will detect and use that.
So, "Load jQuery" is by far the safest and most compatible method, but it means loading one more, slightly different, version of jQuery and Bootstrap.
I hope that helps explain,
Alex