WordPress 3.0.1, for some reason, does not do a proper deactivation/activation cycle on upgrading plugins. Due to database changes in 3.6.0, Breadcrumb NavXT requires a deactivation/activation cycle before it functions correctly. This specifically affects your traditional post and page breadcrumb trails, and a deactivation/activation cycle should clear it up.
Update: It looks like this is caused by the Dashboard > Updates multi plugin updater, use the regular one in Plugins > Plugins.
[end of transmission, stay tuned]