One of the improvements that Apple included in the 10.6.3 update is compatibility with USB input devices. While this may have fixed some problems people were having with third-party mice and keyboards, it seems to have caused problems for other people where device input will periodically pause for about 10 seconds to 15 seconds.
Apple discussion user "Melissa" writes:
"The system still accepts keyboard input (albeit slowly) when the mouse is frozen. The mouse unfreezes after a while (on the order of 30 seconds). The freezing/unfreezing behavior seems to be uncorrelated with my actions. To date, I have had freezing while using Igor Pro, MS Word and Safari, so the problem is not confined to one application."
This problem seems to happen with many Mac models and across applications, indicating the problem is with the software drivers rather than individual applications or hardware.
To troubleshoot this problem, try booting into Safe Mode to see if it the problem continues. Safe Mode stops third-party extensions from loading, so if there is a conflict between Apple's drivers and anything else installed, you should see the problem go away. Additionally, try creating and logging into a new user account. This will help you find out if user settings for drivers are a contributing factor.
If the pauses and slow input still persist, try some of the following fixes:
The first thing you should try if you are experiencing input issues is to reset the system's PRAM. The PRAM holds a number of input-related settings that may be conflicting with driver settings and contributing to the problems. To reset the PRAM, reboot the system while holding the Option-Command-P-R keys all at once, and keep them pressed while the system cycles through a couple of resets. Then release them and allow the system to boot normally.
Reinstall or update third-party mouse drivers
If you have a third-party mouse driver installed, remove it and then reinstall it. You may consider waiting for a driver update as well, since there may be incompatibilities with the USB changes that Apple implemented in 10.6.3 update. Check with the driver developer for information on incompatibilities.
Use alternate drivers
Use Apple's generic drivers
The last option is to uninstall any third-party drivers you have and run your mice and keyboards using Apple's built-in drivers. This may not be the most desired option, but should work while developers work on compatibility fixes.
Remove global account preferences
The global preference file is a hidden file that includes trackpad, mouse, and keyboard settings along with other items such as text substitution settings, recent items, and language settings. Remove this file by entering the following in the Terminal, which will move this file to the Desktop and rename it to be visible in the Finder:
mv ~/Library/Preferences/.GlobalPreferences.plist ~/Desktop/GlobalPreferences.plist
After this is done, log out and back in. Then, check the system preferences for various mouse and keyboard settings and test the input behavior. If the pauses are cleared up, then go about resetting time zones, and other settings for your account: text substitution settings, recent items, languages, system fonts and sizes, text aliasing thresholds, and scroll bar behavior.
If removing and replacing the file does not work, then you can replace it by running the following command:
mv -f ~/Desktop/GlobalPreferences.plist ~/Library/Preferences/.GlobalPreferences.plist