Is that possible that there is some process keep recreating the .htaccess, even thoug the content of .htaccess does not change? Maybe not that specific file, but other .htaccess file along the path.
As lshttpd cache the .htaccess for 10 seconds, then check for changes, reload it if the modified time was changed, if the .htaccess file is being recreated when lshttpd reload the .htaccess, lshttpd may see an incomplete .htaccess without rewrite rules, and that will be cached for about 10 seconds as well.
That's just my guess based on the symtom of the 404 errors, as when 404 errors occur, it will last about a couple seconds then back to normal and all requests to the forum will return 404. You can confirm that with the timestamp of those missing file errors in the error log.
If .htaccess do get recreated once for a while, please make sure to create a temp file and move the temp file to .htaccess, not to overwrite it directly.
I am still trying to reproduce the problem. :-)