Ok, We solved this issue
(First we thought it was due to some extension but we disabled all extensions we installed and it was behaving same)
This comes due to old entries in quote table
We are not sure but some old inactive marked quote item for specific users were causing this delay, perhaps some bug in magento or dont know,
but we removed those entries from quote table which have the customer's email (customer who were facing the timeout issue) and it got fixed,
So basically Old entries some how magento is not be able process or get hold on properly via some queries running on post login pages, causing this issue,
we accidentally found the cause while running
Mysql Show Full process list again and again while it was timing out
So we checked the entry in database and found it was having customer email as logged in user, so to check I deleted that, and Bingo it was solved,
If you guys have came across similar issue and if its not solved by this method but some other method, do share your solution here
