Aman,
I am new to HPLC so any advice I have might be elementary...
Is it possible you have a leak in the system? I have heard you can measure the waste volume to ensure the flow is correct. For example, if the flow rate should be 1 ml/ minute: Move the waste tube to a gradutated cylinder and start a timer, after 10 minutes you should have 10 ml.
Then, If the waste is not 10 mls: either some mobile is lost to a leaky connection or tube, OR it could be the pump is not actually moving the correct amount of mobile from the begining.
We had a connection leak after a technician changed the column. The column was located in a losely covered heating block. I was lucky to check there first, because the very small leak could have evaporated away quickly from the heat and I could have missed it.
Also, I understand it is very common to have leaks in the pump area because there are so many seals.
I hope this helps, Good Luck!