Hosted 2008 SBS, DNS over Site to Site VPN Issues

Hosted 2008 SBS, DNS over Site to Site VPN Issues

Been having a little bit of a headache recently with DNS over site to site
VPN.
We have a SBS within a hosted environment and an RDS. The SBS is of course
hosting DNS for the internal domain. The office has all Domain
Workstations running Windows 7. All seems to run fine until DNS lookups
fail internally, I changed the SBS to have only 127.0.0.1 as primary DNS
(took out a public secondary) and changed the RDS to have only the
internal IP for SBS (again took out a public DNS secondary) and this seems
to have fixed the issue.
My question is why? My thoughts on DNS are:
Workstation - DNS Lookup - DNS Server replies with IP - Workstation can
find machine via IP
So how would changing IP address (secondary) on the Servers affect what
the workstations get as a reply from a DNS query?
Sorry hope this makes sense I tried my best not to waffle!
Thanks,
Charlie H