MySQL optimization - No Innodb support enabled

I just launched my first D7 site. So I'm checking my.cnf settings to make sure they continue to be optimized with the new site. I noticed that there was no Innodb support. I removed the setting to disable innodb but I'm still getting a message when running tuning-primer.sh that no innodb support is enabled. And checking the mysql build it looks like it's there but disabled. What am I doing wrong?

Here is my current my.cnf settings:

[mysqld]
skip-bdb
log_slow_queries = /var/log/mysql/mysql-slow.log
long_query_time = 1
query_cache_type = 1
query_cache_size = 52M
query_cache_limit = 2M
max_allowed_packet = 128M
thread_cache_size = 8
table_cache = 300
key_buffer = 200M
open_files_limit = 1200
max_connections = 100
tmp_table_size = 50M
max_heap_table_size = 50M
join_buffer_size = 512K
read_buffer_size = 256K
sort_buffer_size = 256K
read_rnd_buffer_size = 1500K
myisam_sort_buffer_size = 64M
interactive_timeout = 100
wait_timeout = 120

set-variable=local-infile=0
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql

Default to using old password format for compatibility with mysql 3.x

clients (those using the mysqlclient10 compatibility package).

old_passwords=1

innodb_data_home_dir = /var/lib/mysql
innodb_data_file_path=ibdata1:200M:autoextend
innodb_buffer_pool_size=20M
innodb_additional_mem_pool_size=524288
innodb_log_buffer_size=2M
innodb_thread_concurrency=2
innodb_log_file_size = 256M
innodb_flush_log_at_trx_commit = 2
[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid
skip-bdb

innodb_buffer_pool_size=20M
innodb_additional_mem_pool_size=524288
innodb_log_buffer_size=2M
innodb_thread_concurrency=2
innodb_log_file_size = 256M
innodb_flush_log_at_trx_commit = 2

[mysqldump]
quick
max_allowed_packet = 16M

[mysql]
no-auto-rehash