1. Find out if the Echo canceller is even ON. Sometimes the EC stays off for some reason.

Set echocancel = no, and make a call to a number that you know has bad echo.
Then make it with echocancel = yes. You should notice a _BIG_ difference. If you have to think about it, then there is no real difference and echo cancellation was off both times. The difference should be dramatic.

You can confirm by placing a call and using "zap show channel x" to see the echo cancellation state. If you see that echo cancellation is set to zero taps, then somehow echo cancellation is not enabled. If you see echo cancellation set to 128, 64 or 32 taps, then the global echo cancellation is enabled.

2. If the EC is working, play with the gains.

The software echo cancellers are quite good at reducing echo about 25dB, but you will often have a little echo remaining. This echo residual can be reduced a lot by playing with the tx and rx gains. Try txgain=rxgain=-10 to start. It should have a dramatic effect on the residual echo, at the expense of volume. You can adjust the attenuation and will usually find a setting with reasonable volume and acceptable echo.

3. Limitations of the software EC: The EC in zaptel has been optimized for the lowest system load, so there have been several compromises made. Firstly the training sequence is run much less frequently than in a hardware EC, so training takes 10-15 seconds rather than about 1/4 second. So you will hear echo for the first 10-15 seconds, after which it will largely fade. There is nothing you can do about that in s/w, except use the echotraining feature.
But echotraining does not work on PRI lines. The other problem is that the non-linear processor is missing entirely from the s/w EC so that there is always residual echo that has to be manipulated with the gains.

4. Try decreasing your txgain and rxgain in /etc/asterisk/zapata.conf, and increase the volume on your handsets.

5. You can try a different software echo canceller.
In your zaptel source. modify your zconfig.h file.
Look for #define ECHO_CAN and try a different echo canceller.