It sounds like you're using the same (AD) domain yet you are simply
accepting email for another domain.

That wont be an issue.  The problem you are having with Exchange ActiveSync
is the same exact problem countless other people are having.

A good place to start is in your log files.

First, check to make sure you are logging your ActiveSync connections.  This
will be in IIS on the server you connect to.  Fine the website in IIS that
contains the "Microsoft-Server-ActiveSync" virtual folder.  Turn on logging
for that website if it's not already one.

Now use your iPhone to attempt a connection to your mail server.  Then hunt
down that log file and look for the connection attempt.  The relevant
entries will look like:

OPTIONS /Microsoft-Server-ActiveSync
&Log=VNATNASNC:0A0C0D0FS:0A0C0D0SP:0C0I0S0R0S0L0H 443 DOMAIN\USERNAME
Apple-iPhone/501.345 200 0 0

PROPFIND /exchange/EMAIL
ADDRESS/NON_IPM_SUBTREE/Microsoft-Server-ActiveSync/iPhone/Appl86827DSYY7K -
80 - Microsoft-Server-ActiveSync/6.5.7638.1 401 2 5

POST /Microsoft-Server-ActiveSync
User=USERNAME&DeviceId=Appl86827DSYY7K&DeviceType=iPhone&Cmd=FolderSync&Log=V4TNASNC:0A0C0D0FS:0A0C0D0SP:1C1I465S588RS0L0H0P
443 DOMAIN\USERNAME Apple-iPhone/501.345 500 0 0

These are my errors.  See the 401 2 5 and 500 0 0 at the end of the second
and third entries?  Go to this site to lookup your errors:

http://support.microsoft.com/default.aspx?scid=kb;en-us;318380

Depending on the errors you have (if any) someone else might need to help.
I'm stuck here myself.

At first I thought it an issue with the iPhone not having the proper root
cert for geotrust (rapidssl) but that wasn't it.  Although when I install
the geotrust root cert the iPhone tells me the cert is unsigned.  Which
isn't true.