thanks very much everyone for your advice.
Klarko: i did not find the previous version of wordpressmu to upgrade the versions step by step :(. Also the wordpressmu download page warns about 1.2.4 and previous versions. So assumed it would be ok. I did follow the instructions properly.
andrea_r: 155 blogs
tdjcbe: yes, i did run the upgrade script on the backend
webmaestro: i'll surely check the .htaccess file
In fact i have done the upgrade for the second time from backup. it's still the same.
Also could anyone of you point me to the previous wordpress mu versions so that i can upgrade in sequence.
Also, i'm getting "The connection to the server was reset while the page was loading." errors in the browser when i meant the blogs are unresponsive. I can see the connections to database and also apache and they are not being disconnected.
i'm lost now. Does anyone had this problem of slow loading in 2.6.3 or is it just me?
Thanks