bohman it's very possible that PHP-CGI is contributing to this. Nginx+FPM usually does help, but your concern about htaccess is a valid one. If you can make it work without htaccess then I really recommend FPM.
It's also possible that's not actually your own site causing the problem. If you would like us to look into it then please email support to let us know which site and the date/time/tz that you saw the errors.