We were contacted via our premium support and given a link to this thread. I just did a brief look at WP Security Audit Log's code and I don't see anywhere they open/modify the .htaccess (as WPWhiteSecurity mentioned above) so I don't think it's them.
I also don't think it's us because we use advisory file locking when we edit .htaccess which prevents multiple web server threads from conflicting, or even conflicts with other plugins trying to modify the .htaccess, provided they're also using file locking (flock()).
So... I think it may be another plugin that is not using file locking. My suggestion is to do a search in the source code of all your plugins for ".htaccess" without quotes and where you find they're modifying it, check if they're calling the flock() function before hand to avoid conflicts. If not, you found the culprit.
PS: WPWhiteSecurity sorry to jump your forums, but I hope that helped a little.