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You might be able to see what files the application is writing during first run using something like fseventer.

You could script install/place those files on your clients so that when the app opens for the first time, it doesn't "think" it's the first run.

Disclaimer: I'm not a system admin so this isn't something I've done. You might want to check /r/macsysadmin for people with more experience (although they might recommend a more scalable solution).

Grab a copy of fseventer from http://www.fernlightning.com/doku.php?id=software:fseventer:start

That'll show you all files being accessed/modified in real-time. If it's just the com.cisco.Jabber.plist file that's being modified, ensure that the user logs out after the software is deployed, and logs back in (the file may have been cached).

Are you using version 7? I know the version installed with Final Cut Studio 3 stores the license in: /Library/Application\ Support/ProApps/ProAppsSystemID

Probably not the same but a similar path for 7. You can use a program like fs-eventer to watch what files change on the OS when you enter in and save the license key. Of course, that's if you have a key to enter into a test mac.

Yes, sort of.

OS X has contained a binary for awhile now called fsevents, that keeps track of the file system I/O...so you can see which files in the file system are being accessed while an app is running. And while you can certainly use CLI tools like dtrace to see fsevents, there exists a more approachable and easier-to-use GUI tool called fseventer.

If fseventer is running (and recording/watching), you can launch the problem app in question and it will tell you every single file in the file system that's being opened or read by the app in question, all broken down in a hierarchical tree that shows dependencies and also whether the file(s) were modified, and whether they are only tmp files that were then quickly deleted by the file system.

I've used this many many times to track down a problematic preference file, or to find where an app stores its serialization (sometimes invisible to the Finder; useful for packaging).

With any luck, it may show you a great deal of I/O churn (which could account for the stuttering) and then from there it might give you a clue as to what to target, or remove, or re-install, or force a re-propagation.

You could probably do that with a custom setting. I would have to dig in to find the plist where the settings are set.

fseventer is a good tool for figuring out what changes are being made where. When I am looking to see where I start fseventer then make the change then go look at the file that got touched. From there I can typically determine which setting I need to manage.

There are also places to manage the screensaver. IIRC it is under Login.

edit: moar info!