First of all thank you for showing interest in our plugin.
To start off with, there was already this discussion before which can be accessed from the link below. Just to give you a summary though:
1. WP Security Audit Log plugin does not write to any files in WordPress, or htaccess files, so it is not the plugin that it is doing so.
2. It seems that some other plugins which DO WRITE to htaccess files, or instruct WordPress to write to htaccess files have some incompatibility issue with WP Security Audit Log.
3. We have tried several scenarios (as you can see from the other support ticket) yet we were unable to reproduce the issue.
Therefore if you can make the following test for us it would be great; Enable WP Security Audit Log and start disabling the other plugins one by one. Once the htaccess file is no longer being updated we might have identified the plugin which might be causing such issue.
If you do this test can you please update this ticket?
In the meantime below is the link to the other ticket I referred to in this response: http://wordpress.org/support/topic/htaccess-file-corruption