If you ever install MySQL on Mac OS X and get some troubles with it, usually first step that will taken is reinstall it. Because uninstall MySQL on Mac OS X is not a easy, usually we will reinstall it directly. Unfortunately, MySQL installer always reinstalls existing MySQL with upgrade mode. In my experiences, if you're continuing in upgrade mode, it cannot solve the problem. I suggest you to reinstall it in fresh installation, with that mode MySQL will overwrite all its files with new one. And I can’t warranty if it always solving your MySQL troubles but according my experiments, for several times, reinstall in fresh installation mode, the problem will solved.

But how do to install it in fresh install mode? MySQL will display the Upgrade button on installation screen, if you have an existing MySQL in your system.
To solves this problem, you have to login as Administrator to do this. Mac OS X will put every .pkg files in /Library/Receipts/ folder.
To go there you can use Finder or Terminal. If you're using Finder, go to Macintosh HD - Library - Receipts folder then find file mysql-5.0.45-osx10.4-i686.pkg (because my existing MySQL version is 5.0.45, so the file name may vary, if your existing MySQL version 5.0.41 so your files has name mysql-5.0.41-osx10.4-i686.pkg) then delete that file.
Or if you're using Terminal, open your Terminal first then at prompt type cd /Library/Receipts. If you already in there, type cd mysql-5.0.45-osx10.4-i686.pkg (or you can type cd mysql(then press TAB key here to completed the file name, you can type it repeatly until you find the file) and then use commands rm and rmdir in that folder to delete files and folders, you can use wildcard for files, like rm *.*.
After file mysql-5.x.xx-osx10.4-i686.pkg already removed, try to execute MySQL installer again then you get Install button in there to make fresh install.

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