InnoDB to MyISAM Conversion Problem
Setting skip-innodb does disable the InnoDB Storage Engine, but that does not convert the tables. 

You need to script the conversion of all the tables.

STEP #1

Comment out the skip-innodb

[mysqld]
#skip-innodb


STEP #2

service mysql restart


STEP #3

Execute the Following Script snf View Results

CONVERT_SCRIPT=/tmp/InnoDBConversionToMyISAM.sql
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') "
SQL="${SQL} FROM information_schema.tables "
SQL="${SQL} WHERE engine='InnoDB' AND table_schema &lt;&gt; 'mysql'"
mysql -uroot -p -ANe"${SQL}" &gt; ${CONVERT_SCRIPT}


STEP #4

View the script

vi /tmp/InnoDBConversionToMyISAM.sql


or

less /tmp/InnoDBConversionToMyISAM.sql


If you like the contents, then ...

STEP #5

Login to mysql and run

mysql&gt; source /tmp/InnoDBConversionToMyISAM.sql


STEP #6

Uncomment out the skip-innodb

[mysqld]
skip-innodb


STEP #7

service mysql restart


STEP #8

There is no STEP 8. That's it !!!

Give it a Try !!!