EDIT: the IIRF.ini code was not the problem in this case, the performance issues with dokuwiki were in fact permissions related, and the introduction of URL re-writing was not the cause of the issue.
I've got a new instance of Dokuwiki (i.e. almost empty, not in use) which was running perfectly fine, before I integrated URL-rewriting using IIRF.
It now runs significantly more slowly - navigating between pages takes a number of seconds whereas before it was 'snappy' (immediate).
I followed the directions for implementing IIRF here, which basically involves adding an "IIRF.ini" file to the site root, and updating the "conf/local.php" file as instructed on the site linked above (code copied from under the heading "Ionics Isapi Rewrite Filter").
So to clarify, URL-rewriting is working; but it's caused significant slow-down in navigating the wiki. I'd appreciate it if anyone could offer a suggestion for bringing it up to speed again!
This is the contents of my "IIRF.ini" file:
IterationLimit 1
# QSA is not supported, fix it
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule (.*)\?(.*) $1&$2
RewriteRule ^/_media/(.*) /lib/exe/fetch.php?media=$1 [QSA,L]
RewriteRule ^/_detail/(.*) /lib/exe/detail.php?media=$1 [QSA,L]
RewriteRule ^/_export/([^/]+)/(.*) /doku.php?do=export_$1&id=$2 [QSA,L]
RewriteRule ^/$ /doku.php [QSA,L]
# infinite redirect fix
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^/(.*)/$ /doku.php?id=$1 [QSA,L]
# end fix
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^/(.*) /doku.php?id=$1 [QSA,L]