The problem with proximity sensor is described better in these threads on XDA: first and second. Basically, phone's screen stays off during calls, no matter whether it's on the ear or in your hand.
I found that there are differences between my phone and the others: If I tried to count correct value to write to /efs/prox_cal I always got 0. That value changed nothing. Then I tried value from the first thread which is 45 in hex and that worked. But somehow the value wouldn't persist through reboots. So I rolled my own solution which is to write custom init script. I'm running AMCHA Rom 9.0 (based on stock) if it matters.
mount -o remount,rw /system
cd /etc/init.d
vi 20fixproximity
#!/system/bin/sh echo -en $'\x45' > /efs/prox_cal chown system:system /efs/prox_cal chmod 644 /efs/prox_cal