Hi,
Aikijujutsu is one of a myriad of terms used by varying schools over Japan's history. Others include Yawara, Te, Goho, Jujutsu, Taijutsu, Koppo, Dakentaijutsu, Wa, and Hada, although this is still not an exhaustive list. Probably the best known school using this particular term is the Daito Ryu, which formed the basis for most of Aikido's technical curriculuum (for the unarmed, at least).
Without getting into it too much, the particular terminology and name(s) used by a school doesn't necessarily imply or define the technical side of things. Two different schools using the same name may be similar, but may just as likely be completely unrelated. The Daito Ryu's expression of the term "Aikijujutsu" includes a circular approach, with some incredibly painful pins, locks and limb controls. Unlike many other Japanese systems, it also has a very healthy emphasis on Atemi, or striking, usually to set up throws and other grappling techniques.
To address Jarrod's experience, the Daito Ryu (as with many classical Japanese arts) has an emphasis on standing grappling, rather than ground work, and will teach in a manner similar to the KJJR you have experienced (drilled techniques).
So the real question would be "What is the emphasis of x-Ryu Aikijujutsu, and how does that differ from KJJR?", and the answer will be determined by the particular school we are discussing. If it is the Daito Ryu you are asking about, well, as it is a single art, and the KJJR syllabus is taken from a number of sources, then there will probably be a bit of noticable difference in the way the art is approached, but there will be little difference in the technical aspects. From memory, the KJJR includes Daito Ryu Aikijujutsu in it's list of arts, so it's in there for you already, just not as an individual study in the mainstream.
Hope this has been of some help, any Daito Ryu guys here can probably help a lot more and point out anything I may have gotten wrong...