Updated to the latest JFBC V4.3.4 and JLinked v1.4.1 for Joomla2.5...everything is back to working normally, Autotune runs correctly, and my SC Subscriber ID is being recognized correctly. Thanks for all your help!
Fantastic! Very glad to hear we helped you get past this, and sorry for the troubles. The next releases of JFBConnect and JLinked will share even more code, which will hopefully prevent these oddities going forward.. but if not, we'll always be here to help.