DirectoryIndex index.php
RewriteEngine On
# Редиректы
RewriteCond %{HTTP_HOST} ^(.*)$ [NC]
RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteRule ^(.*)$ http://www.%1/$1 [R=301,L]
RewriteRule ^page/([0-9]+)(/?)$ index.php?cstart=$1 [L]
# Сам пост
RewriteRule ^([0-9]{4})/([0-9]{2})/([0-9]{2})/page,([0-9]+),([0-9]+),(.*).html$ index.php?subaction=showfull&year=$1&month=$2&day=$3&news_page=$4&cstart=$5&news_name=$6&seourl=$6 [L]
RewriteRule ^([0-9]{4})/([0-9]{2})/([0-9]{2})/page,([0-9]+),(.*).html$ index.php?subaction=showfull&year=$1&month=$2&day=$3&news_page=$4&news_name=$5&seourl=$5 [L]
RewriteRule ^([0-9]{4})/([0-9]{2})/([0-9]{2})/print:page,([0-9]+),(.*).html$ engine/print.php?subaction=showfull&year=$1&month=$2&day=$3&news_page=$4&news_name=$5&seourl=$5 [L]
RewriteRule ^([0-9]{4})/([0-9]{2})/([0-9]{2})/(.*).html$ index.php?subaction=showfull&year=$1&month=$2&day=$3&news_name=$4&seourl=$4 [L]
RewriteRule ^([^.]+)/page,([0-9]+),([0-9]+),([0-9]+)/(.*)/$ index.php?newsid=$4&news_page=$2&cstart=$3&seourl=$5&seocat=$1 [L]
RewriteRule ^([^.]+)/page,([0-9]+),([0-9]+)/(.*)/$ index.php?newsid=$3&news_page=$2&seourl=$4&seocat=$1 [L]
RewriteRule ^([^.]+)/print:page,([0-9]+),([0-9]+)/(.*)/$ engine/print.php?news_page=$2&newsid=$3&seourl=$4&seocat=$1 [L]
RewriteRule ^([^.]+)/([0-9]+)/(.*)/$ index.php?newsid=$2&seourl=$3&seocat=$1 [L]
RewriteRule ^page,([0-9]+),([0-9]+),([0-9]+)/(.*)/$ index.php?newsid=$3&news_page=$1&cstart=$2&seourl=$4 [L]
RewriteRule ^page,([0-9]+),([0-9]+)/(.*)/$ index.php?newsid=$2&news_page=$1&seourl=$3 [L]
RewriteRule ^print:page,([0-9]+),([0-9]+)/(.*)/$ engine/print.php?news_page=$1&newsid=$2&seourl=$3 [L]
RewriteRule ^([0-9]+)/(.*)/$ index.php?newsid=$1&seourl=$2 [L]
# поиск по доп полям
RewriteRule ^search/(.*)/page/([0-9]+)(/?)+$ index.php?do=xfsearch&xf=$1&cstart=$2 [L]
RewriteRule ^search/(.*)/?$ index.php?do=xfsearch&xf=$1 [L]
# вывод для отдельного юзера
RewriteRule ^user/([^/]*)/rss.xml$ engine/rss.php?subaction=allnews&user=$1 [L]
RewriteRule ^user/([^/]*)(/?)+$ index.php?subaction=userinfo&user=$1 [L]
RewriteRule ^user/([^/]*)/page/([0-9]+)(/?)+$ index.php?subaction=userinfo&user=$1&cstart=$2 [L]
RewriteRule ^user/([^/]*)/news(/?)+$ index.php?subaction=allnews&user=$1 [L]
RewriteRule ^user/([^/]*)/news/page/([0-9]+)(/?)+$ index.php?subaction=allnews&user=$1&cstart=$2 [L]
RewriteRule ^user/([^/]*)/news/rss.xml(/?)+$ engine/rss.php?subaction=allnews&user=$1 [L]
# вывод всех последних новостей
RewriteRule ^lastnews(/?)+$ index.php?do=lastnews [L]
RewriteRule ^lastnews/page/([0-9]+)(/?)+$ index.php?do=lastnews&cstart=$1 [L]
# вывод в виде каталога
RewriteRule ^catalog/([^/]*)/rss.xml$ engine/rss.php?catalog=$1 [L]
RewriteRule ^catalog/([^/]*)(/?)+$ index.php?catalog=$1 [L]
RewriteRule ^catalog/([^/]*)/page/([0-9]+)(/?)+$ index.php?catalog=$1&cstart=$2 [L]
# вывод непрочитанных статей
RewriteRule ^newposts(/?)+$ index.php?subaction=newposts [L]
RewriteRule ^newposts/page/([0-9]+)(/?)+$ index.php?subaction=newposts&cstart=$1 [L]
# вывод избранных статей
RewriteRule ^favorites(/?)+$ index.php?do=favorites [L]
RewriteRule ^favorites/page/([0-9]+)(/?)+$ index.php?do=favorites&cstart=$1 [L]
RewriteRule ^rules.html$ index.php?do=rules [L]
# RewriteRule ^statistics.html$ index.php?do=stats [L]
RewriteRule ^addnews.html$ index.php?do=addnews [L]
RewriteRule ^rss.xml$ engine/rss.php [L]
RewriteRule ^sitemap.xml$ uploads/sitemap.xml [L]
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^([^.]+)/page/([0-9]+)(/?)+$ index.php?do=cat&category=$1&cstart=$2 [L]
RewriteRule ^([^.]+)/?$ index.php?do=cat&category=$1 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^([^.]+)/rss.xml$ engine/rss.php?do=cat&category=$1 [L]
RewriteRule ^page,([0-9]+),([^/]+).html$ index.php?do=static&page=$2&news_page=$1&seourl=$2 [L]
RewriteRule ^print:([^/]+).html$ engine/print.php?do=static&page=$1&seourl=$1 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^([^/]+).html$ index.php?do=static&page=$1&seourl=$1 [L]
в них и надо смотреть что и как было изменено в двиге, и смотреть на что это всё может влиять! Ставь коробочный чистый вариант, и начинай делать правки заново, проверяя каждый раз после изменений в двиге работу пагинации всех разделов... Иначе никак не выявить виновника сей проблемы