MySQL ignoring some params from my.cnf
I had a similar problem with a box I was diagnosing for performance issues, it turned out that there was an incorrect / misplaced heading entry within the my.cnf for that server, so MySQL was ignoring all the settings within that section...

For example, if you had the following;

[mysqld]
######################################################
# First, the generic server configuration items
port                    = 3306
socket                  = /var/lib/mysql/mysql.sock
datadir                 = /mysql/data

[client]
#password               = your_password
port                    = 3306
socket                  = /var/lib/mysql/mysql.sock

key_buffer_size         = 256M
table_open_cache        = 1024
query_cache_size        = 32M


Then the buffer tuning section is ignored as it is within the client section and not the mysqld section... Re-arrange the sections, and all works as intended.

Hopefully, it is as simple as this for you!