My.cnf Have Delete The Table

i have update my.cnf with the following configuration and now i have a lor of customer that have lost him table, seem that this configuration have delete in random .Myi files, i would put this my.cnf also on others server but i would undestand which setting in this .cnf make problem for the table.

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
skip-locking
skip-innodb
#skip-networking
safe-show-database
query_cache_limit=1M
query_cache_size=96M ## 32MB for every 1GB of RAM
query_cache_type=1
max_user_connections=200
max_connections=500
interactive_timeout=10
wait_timeout=20
connect_timeout=20
thread_cache_size=128
key_buffer=384M ## 128MB for every 1GB of RAM
join_buffer=1M
max_connect_errors=20
max_allowed_packet=16M
table_cache=1024
record_buffer=1M
sort_buffer_size=3M ## 1MB for every 1GB of RAM
read_buffer_size=3M ## 1MB for every 1GB of RAM
read_rnd_buffer_size=3M ## 1MB for every 1GB of RAM
thread_concurrency=2 ## Number of CPUs x 2
myisam_sort_buffer_size=64M
server-id=1
log_slow_queries=/var/log/mysql-slow-queries.log
long_query_time=2
collation-server=latin1_general_ci

[mysql.server]
user=mysql
#basedir=/var/lib

[safe_mysqld]
err-log=/var/log/mysqld.log
pid-file=/var/lib/mysql/mysql.pid
open_files_limit=8192

[mysqldump]
quick
max_allowed_packet=16M

[mysql]
no-auto-rehash
#safe-updates

[isamchk]
key_buffer=64M
sort_buffer=64M
read_buffer=16M
write_buffer=16M

[myisamchk]
key_buffer=64M
sort_buffer=64M
read_buffer=16M
write_buffer=16M

[mysqlhotcopy]
interactive-timeout