Its sounds like your T1 is slipping, basically its losing synchronization and frames are getting corrupted, dropped, etc..
So to make sure its timed right you need to setup the clock source, and setup the clock slaving..
You want to clock from the most central point you can. Your central point being your headend router..
First thing, do you have internal or external DSU/CSU's?
If internal and they're the WIC-1DSU-T1 modules you can do a command on the headend router like "service-module t1 clock source internal" and at the remote site, do "service-module t1 clock source line"
The "service-module t1 clock source line" is on by defualt, and probably doesn't need to be changed at the remote site (it also won't show up in the config)
If you have external DSU's you need to set them up manually through the dsu admin panel. Headend being the clock source and remote to synch from the line.
Hope this helps
BuckWeet