I have been having the same issue with my 3GS with AT&T and have been working closely with them since the beginning of November. I have had the SIM replace, the phone replace, the software restored from scratch two times and my Jawbone Prime replaced and it still does the same thing, more than 50% of my calls were dropping. I spoke with a collegue of mine and he recommended turning off 3G. When I did my call drop count went from 50% to 0%. I have an exsisting case going with AT&T and not one time did they suggest doing this.
If you are experiencing issues with dropped calls, download the AT&T Mark the Spot Application and send all of your dropped call issues to AT&T. If you do not report the dropped calls then they advertise that they have less dropped calls than any other vendor, which is trues because they have made it virtually impossible to report a dropped call from the location of the dropped call, unless you happen to carry two phones.
It is hard to trouble shoot an issue if it is never reported.