FURL takes over on sub directories

Hola all,
I have a site with FURL and SEO strict plugin.
modx is installed in the root. beside modx I also have other apps like lime survey and OpenGoo in sub directory under modx, ie http://site.com/survey/ and http://site.com/opengoo but now when I try to access these pages I’m getting my custom 404 page error.

if I disable my .htaccess it’s all back to normal.
is there a directive specific to exclude certain paths from FURLS?

Put another .htaccess in the affected folders like the one in the /manager folder; it turns off the rewrite engine for the folder it’s in (and its children).

thx Susan. I tried your suggestions and also tried

and it’s working. but if I have password protected folder (like the limesurvey admin interface) I still get the 404 page.
if my main .htaccess is commented out they the browser gives me the login prompt.
so I would say it’s working unless the dir is password protected with .htpasswd

any ideas?