There were indeed severe problems with having two versions. The automatic MySQL start was not working and I could not start it from a command line. I use a Mac G5, unix based open source. I dumped the 4.1.16 but still could not access MySQL through PHP code. Then I dumped the 4.0.24 thus eliminating all MySQLs.
The problem began when I "upgraded" MySQL without shutting down and dumping the one installed. The newer version requested a CANCEL or UPGRADE, something that should not be done, at least with a Mac. Once I recognized this and did the above, the 4.0.24 then requested CANCEL or INSTALL! Voila! Everything began working fine. I adjusted the config.inc.php file and my PHP connect file to match username and password. Database comes up great with phpMyAdmin and the browsers all see it OK.
The Read Me Txt file that comes with a newer MySQL version pkg could stand a revision. There are instructions that tell you to do something, and after you've done it and continue reading, it says, "Before you do this, do . . ." Getting the cart before the horse seems to be in a lot of instructions.