Erratic behaviour after transfering user from PowerPC (G5)

After getting my new MBP a few weeks ago I transferred most of the user data from my old Mac, a PowerMac G5.
From day one the machine seems to have displayed erratic behaviour at times, and there seems to be a small "lag" at times, for example when scrolling through files.
Today I also got a weird java-problem, which disappeared in the new, fresh test user I created ...
Could something have gone wrong in the user transfer process? Is there an easy fix here, or do I have to reinstall?
I have already done the usual things (disk repair, Cocktail processes etc.), but nothing helps.

How did you transfer data? Did you follow Kappy's and a brody's guide to migrating?
http://discussions.apple.com/thread.jspa?threadID=435350&tstart=10

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A Basic Guide for Migrating to Intel-Macs
If you are migrating a PowerPC system (G3, G4, or G5) to an Intel-Mac be careful what you migrate. Keep in mind that some items that may get transferred will not work on Intel machines and may end up causing your computer's operating system to malfunction.
Rosetta supports "software that runs on the PowerPC G3 or G4 processor that are built for Mac OS X". This excludes the items that are not universal binaries or simply will not work in Rosetta:
Classic Environment, and subsequently any Mac OS 9 or earlier applications
Screensavers written for the PowerPC
System Preference add-ons
All Unsanity Haxies
Browser and other plug-ins
Contextual Menu Items
Applications which specifically require the PowerPC G5
Kernel extensions
Java applications with JNI (PowerPC) libraries
See also What Can Be Translated by Rosetta.
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The same problem will exist for any hardware drivers such as mouse software unless the drivers have been compiled as universal binaries. For third-party mice the current choices are USB Overdrive or SteerMouse. Contact the developer or manufacturer of your third-party mouse software to find out when a universal binary version will be available.
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Apple Guide to Universal Applications
MacInTouch List of Compatible Universal Binaries
MacInTouch List of Rosetta Compatible Applications
MacUpdate List of Intel-Compatible Software
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In your /Home/Library/ folder:
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Erratic behaviour after transfering user from PowerPC (G5)

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