This is well known issue, Magento need to patch .htaccess file as well as its sample file (.htaccess.sample). If you use a modified .htaccess file you have to run something like this:
mv .htaccess .htaccess_original
wget -qO .htaccess http://svn.magentocommerce.com/source/branches/1.7/.htaccess
wget -qO .htaccess.sample http://svn.magentocommerce.com/source/branches/1.7/.htaccess.sample
sh PATCH_SUPEE-6788_CE_1.9.1.0_v1-2015-10-27-09-06-11.sh
mv .htaccess .htaccess_patched
mv .htaccess_original .htaccess
Do not forget to use the correct patch filename.
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