Did Better WP security crash my site?

Hi,
I not sure but it seems that the Better WP Security crashed my site (4 times!). My htacess was changed all the times (deleted piece of content or insert non readable characters. Previously I was sure my site was hacked… But I didn’t found any sighs of hacking in same time Better WP Security didn’t say anything.
Next I switched off most of the function but today situation repeated.
Of course I not sure for 100% and decided to check it by deactivating the plugin and see (will this situation repeat or not).
I never switch on automatic write to htaccess or wp-config. And added all functions manually. So I not sure that there is no function left after Better WP Security. Could you check it please:

suPHP_ConfigPath /home/[skipped]
<Files 403.shtml>
order allow,deny
allow from all
</Files>
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
</IfModule>
# END WordPress

http://wordpress.org/plugins/better-wp-security/