I've had a lot of problems with ATA's and faxing so I can sympathize.
Make sure QoS is properly configured on you Gb links. This is vital.
Use the 2.16.1 code on the ATA's. Earlier versions have lots of bugs. This version is solid.
Disable fax relay. I never could get this to work reliably.
Make sure you are using the G.711 codec for your remote sites.
Turn on Fax/Modem Packet Redundancy. This takes 2-4 times the bandwidth but was key to getting things working.
Use an IOS NSE type, not non-IOS. This should be the default if you are using an IOS gateway but in my case I'm using a Catalyst 6513 with a 6608 PRI card and the default was non-IOS. This was also critical for getting VG-248's working correctly. (Use the latest code for them also!)