I gotta agree with MisterMe here -- Apple does NOT keep all UNIX components of Mac OS X up-to-date with the latest versions available. Apple has put together a very stable collection of UNIX programs, some of which are not the latest versions available... we can only speculate as to why, but you can see from your experiences that trying to install the latest and greatest versions does not always work.
Unless there is some dire need for some feature of CUPS that isn't available with the CUPS that comes standard with Mac OS X, then I would suggest just letting Apple do the updating. If there's a CUPS update that needs to be applied, Apple will supply it in the form of a Software Update (and it may or may not read "CUPS" in the update -- it may simply read "Printer Update" or something similar).
Even though the Print & Fax control panel looks nothing like CUPS, it does, indeed, use CUPS as the printing subsystem -- it's just hidden away so that casual users who are not familiar with either UNIX or the command line don't have to worry about complex stuff like that.
Apple has done a fantastic job of hiding the complexity of UNIX from the casual Mac OS X user. While I understand that power users and UNIX gurus would like to get their hands on the UNIX underpinnings of Mac OS X, Mac OS X just wasn't designed with the UNIX tinkerer in mind. If you so choose to dive into the UNIX underpinnings of OS X and start changing things like CUPS, then you will run into headaches along the way, and possibly "break" stuff that may be dependent on what you're changing.
I understand that there is a need, sometimes, to get something to work, and it would require diving into the UNIX underpinnings of Mac OS X. Just be aware that this isn't condoned by Apple (especially replacing the entire CUPS system with a newer version), since, as we all know, software changes over time, and the newer version you're installing may have changes that are not compatible with the other systems in Mac OS X that rely on CUPS.
Sorry about the ramble, just went off for a sec there... whew!
