That behavior doesn't make much sense - the domain of the sender
shouldn't make any difference, and certainly whether they are in a
sub-domain or should not. My best guess is there's a routing issue
somewhere along the line for the sender domains that doesn't work. Are
you sure the ones that fail are not sub-domains of the same domain you
are sending to? If so, that wouldn't be all that uncommon, as getting
those settings right for mail delivery tend to be trickier than for
outside domains.

The thing is whenever mail is sent from
multi-domain id, it comes in the drop folder of "mailroot" folder in sharepoint.
So how can it be a routing issue? The problem starts from this point. From drop
folder, it is diverted to somewhere. how can we track that?

What I'm saying is that the source of the message shouldn't have
anything to do with what happens once you get to the final mail server
in the chain. What the final server ends up being is a function of how
your routing is setup.

Are you saying that all of the messages end up in the same drop folder,
but from there things are handled differently? If so, check the ULS log
for your SharePoint server - if something is fail at the time the
messages are picked up from the dropbox, an error/warning will be logged
there.

I did the below change in the form Library settings.
Form Library settings --> Incoming E-Mail Settings --> Save Original E-Mail?
(Yes) (previously it was "no")

By making the above change I am getting the E-mail without any
attachment. Can you please help me out in finding the reason behind this? do we
have any setting in sharepoint to remove the attachment from the E-Mail?

Whether you get the attachment or not depends on a few things - the most
important bits are what kind of list/library the email  is ending up in,
and what kind of attachment the email includes.

Thanks for showing an interest in solving my issue. I am using the form
library and an email  includes an xml document. Also I checked that xml extension
is not blocked in the central admin.

I am able to send the mail using the yahoo.com domain but this problem
only occurs with sub domain mail id.

Are you certain the attachment isn't being removed by one of the mail
servers along the way? If it was being stripped out by SharePoint, you
should see an error in the ULS log that would tell you why.