(Solved already, writing this for the next guy)

I noticed that whenever I start Winamp it notifies me that a new version is available, even though I go to Options->Preferences and uncheck the checkbox saying "Check for new version of Winamp at startup"

After some testing, I realized that after unchecking the checkbox, then closing and re-opening Winamp, the checkbox is once again checked.

How can I turn off the new version notification permanently?

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As it turns out, if I also uncheck the option "Allow Winamp to report anonymous usage statistics", the preferences are saved correctly.

Alternatively, you can disable the internet connection entirely - choose "Not connected to the internet" under "Select you internet connection". (From here).

Lastly, you can manually edit the preferences file by running

notepad "%APPDATA%\Winamp\winamp.ini"

From Start->Run (under XP)

Then change the line

newverchk2=1

to

newverchk2=0
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