I own a 2001 Accord and my hubby owned a 93 Civic and we have had some rotor warping(or least what I think was warping-read the link!!). For a long time I thought it was many other things--struts, tires, etc. but I found out that a warped rotor could be the culprit. After much deliberation and posting in several forums, I ordered the Brembo replacement rotors from Tirerack.com. Drilled or slotted are a complete and total waste of money unless you are a serious racer or have a show car. They also can wear down your pads quicker.

Read the article linked--it will at least help you with the bed-in process which could be contributing to your problem, as well. Warped rotor myth

As a side note, my rotors have been on for several months and driven a lot and are still going strong. The replaced rotors have helped tremendously, but have not fixed the problem to perfection. The car is a daily driver and 99% better is good enough for me!