On September 18th, Martyn Plummer updated rjags. Normally, this wouldn't be a big deal, but a question came across the R-sig-debian mailing list about the package at the same time, and I noticed that my Ubuntu 12.04 (precise) machine was using version 3.3 from the Ubuntu universe repository and not the 3.5 version that is available at the RRutter or c2d4u PPAs.
Turns out the version numbering system used by Martyn is not compatible with the Ubuntu numbering system used for the package in the universe repository. The universe package is numbered "3.3" while Matryn's numbering format uses all dashes, "3-5". The debian version of the package has not been updated since 3.3, so the source package used to create my update was genereated via the cran2deb4ubuntu project and kept Martyn's "-" version numbering.
Even though rjags 3-5 was available in the PPA, rjags 3.3 was considered a more recent version by Ubuntu and the package was never upgraded. It is possible to use apt pinning or synaptic to force the "newer" version, but I have correct the numbering issue and the newest version of r-cran-jags is numbered "3.7" and will update automatically.
Not sure if any other packages on c2d4u have similar issues. If anybody spots one, please let me know.