Crackling noise could simply be corrosion on the contacts of the module. I would try simply removing the modules and then re-seating them.
It could also be errors on the PRI. You can test this by placing a call from one FXS port to another (by dialing the IN#ACCEPT of the other FXS port) and see if there is any noise when the call is only processed by the ATLAS and does not go out or come in on the PRI. If there is no noise when dialing FXS to FXS but there is noise when it goes over the PRI, then the noise is coming from the PRI and may be due to errors or clock slips.
You can look to see what errors are being detected on the PRI by looking under MODULES, and going into the MENU for the T1/PRI module, and then looking at the PERFORMANCE statistics (Current, 15 minute, and 24 hour). These list the possible errors, so any values are physical layer errors that have been detected. If it is all zeros then there have been no errors.