I just upgraded to official release of 6.0.0.415 on my 9650 and know no one can hear me when I talk to them thru the built in microphone, but all is OK when I am on Bluetooth.
I have had this same issue with multiple 9650's and on all releases (even betas) of OS6.
I upgraded several days ago and have had no issues with the microphone not working on my 9650. Perhaps wipe & install again, in case something went awry during the install?
The issues seem to be that it does not release the Bluetooth mic, I have had 3 different 9650's and all have the same issue on many different release of OS6
Issues with the speaker mike not working after an upgrade seem to be common. RIM suggests a reload of the OS. I would suggest it be done from the PC not OTA.