Apart from the advice i'm offering, i cant help.
I would until more help comes along,
try checking the permissions manually.
I do know that not all directories are covered by
the cp permissions checker. And i not sure about the istaller.
But checking the permissions i guess is going to be the first thing to check.
-----
Can you check your log file?
You have a Admin and Mysql Log File?
Set these up if you havnt via the cp and hopefully
they may offer more help.