Well, I'm on an XP machine and for developing mysql/php sites I use either phpdev or xampp. When I startup phpdev and create a table, it all works fine (same goes for xampp).
But if I startup both (or one doesn't shut down properly), it will also load mysql.exe twice.
Changes made in one mysql.exe are unknown to the other and thus unreadable by other software (phpMyAdmin, WinMySQLAdmin,...)
So possibly it's the same story in your case.