Remote connection issues via T-1

We have a Win 2003 server and have access from 3 remote offices via t-1 lines
and cisco routers. At one location we are able to connect via remote desktop
to our terminal server and run apps with no problems. However, if we bypass
terminal services and try to access the applications on the Windows server
directly we are unable to run any apps we can also not copy any files that
are larger then 2 meg. We get a Windows delayed write errors that says we
have lost our network connection. However, clicking on my computer shows that
we are still connected. We have had the T-1 tested from point to point and
phone company can find no problems. The routers are pretty much configured
all the same at all locations so we are pretty sure it is not a router issue.
Swapped out switches, routers, patch cables tried just connecting 1 computer
to the router and still cannot run any apps. Any ideas are appreciated as
this is the strangest problem I have seen in 15 years of networking. We know
it is not a rights issue as we are logging in as administrator.