U're right, updating of the library might not be the culprit.
It never hurts to repair the library occasionally for maintainance purposes, and to get it out of the way, when debugging. But your problem seems to be system wide.
I still suspect, you may have installed some third party software on both machines, some nice innocent helper application, that is now causing trouble. Do you use any non-Apple add-ons, older programs that have not been tested with Lion or Mt. Lion?
@Kirby, do you have a brainwave, if you are still following this thread? I am quickly running out of ideas.
We need clues.
@lucky.lucb,
Do you have a "Console" window open? If not, launch the Console application from the Applications > Utilities folder and have a look, if diagnostics or error messages appear, when you try to group the projects by year or by folder. If yes, then post the message here.
Couldn't the bug be here : when accessing with "Aperture 3.4.3" to "iPhoto 9.4.2"-updated libraries ?
There is a known bug, that sorting of projects by date does not work, if the Aperture library contains smart albums that have been created in iPhoto. If you still have smart albums, that you imported from older iPhoto libraries, then replace them by recreating the same album in Aperture. But I do not see, how this could help here, since you said, that you tested with new libaries on both machines.
Please post back, if you find something in the Console.
Regards
Léonie