neha123,
My wife also had the same problem. But when we were filing for I-485, my lawyer pointed out that this could be a slight problem as the rule is that we have to start working on H1 before 90 days. At that time she was had completed almost 120 days in H1.
So what we did is: we went outside the country (Canada) and came back and requested for a new I-94. So they gave her an I-94 based on her H4 stamped in the passport(we hadn't yet stamped the H1).
Anyways, I do not think this is a problem for INS. Even though it comes as a problem, you can use 245(i).
Good luck. I hope that your misery is almost going to end
RD:06/01/01
ND:08/25/01
FP:05/17/03