If they are digital trunks then you may want to get your SP involved to verify the trunks. The 3300 also has the capability of hardware or software-based echo cancellers, each with their own merit. That however is something best left to their support to figure out.
If it's a digital trunk, one of two things are happening. Either there is too much echo for the system to suppress, or there is a small amount of echo, so small that the echo cancellers don't detect it but when you add the IP delay, it's noticeable to the user.
There is a third reason, and that is that the far end is on a cell phone or hands-free device. Make sure you do a test call to a well known POTS device to make sure it's not user error on the far end...