Hi,
my guess is that it could be due to email is not send directly to primary SMTP which is configured in email router for your queue, it could be possible this email is send to other alias and if this is the case CRM ignores those email.
for e.g. here is how you mail box is set up
support@yourcompanyname.com (mail box, primary SMTP, configured as queue in CRM to send recieve mail )
service@yourcompany.com (alias for above mailbox)
so if email is send to "service@yourcompany.com" it will be received in outlook mail box but CRM will not pick it as it does not have any matching queue set up for this.
MayankP
My Blog
Follow Me on Twitter