(Even though it didn't happen on my install...anyways, the rewrite rule also only steps into effect if $serendipity['indexFile'] != 'index.php', we may want to create a conditional rule here.
RewriteRule ^{PAT_SEARCH} {indexFile}?url=/{PATH_SEARCH}/$1 [L,QSA]
RewriteRule ^{PAT_CSS} {indexFile}?url=/$1 [L,QSA]
RewriteRule ^{PAT_AUTHORS} {indexFile}?url=/{PATH_AUTHORS}/$1 [L,QSA]
-RewriteRule ^index\.(html?|php.?) {indexFile}?url=index.html [L,QSA]
+RewriteRule ^index\.(html?|php.+) {indexFile}?url=index.html [L,QSA]
RewriteRule ^htmlarea/(.*) htmlarea/$1 [L,QSA]
RewriteRule (.*\.html?) {indexFile}?url=/$1 [L,QSA]
RewriteRule ^{PAT_SEARCH} {indexFile}?url=/{PATH_SEARCH}/$1 [L,QSA]
RewriteRule ^{PAT_CSS} {indexFile}?url=/$1 [L,QSA]
RewriteRule ^{PAT_AUTHORS} {indexFile}?url=/{PATH_AUTHORS}/$1 [L,QSA]
-RewriteRule ^index\.(html?|php.?) {indexFile}?url=index.html [L,QSA]
+RewriteRule ^index\.(html?|php.+) {indexFile}?url=index.html [L,QSA]
RewriteRule ^htmlarea/(.*) htmlarea/$1 [L,QSA]
RewriteRule (.*\.html?) {indexFile}?url=/$1 [L,QSA]