@blakespott
There are many discussions about Update 3 on amigaworld.
If you have a backup of your previous Update 2 installation, I would suggest copying your backup version of Devs/Monitors/Radeon file over to your new Update 3 Devs/Monitors drawer.
This will allow you to use the previous settings for your Radeon card and montior.
As a last resort, I would suggest doing the following to create a "pure" install:
1) Quick format of your system partition (only the OS4 partition).
2) Install AmigaOS 4.1 Update 1 from CD
3) Download and install AmigaOS 4.1 Update 2 from Hyperion web site
4) Download and install AmigaOS 4.1 Update 3 from Hyperion web site
Please note that I have a MicroA1, so I am not sure if there were any "fixes" for the SAM that might be needed in addition to the above updates.
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redfox