We have a scheduled task which runs every 5mins and sends pending email campaign.

The scipt has been written in VB and following is the code which actually sends the mail:
set mailer = createobject("cdo.message")
mailer.subject = this_subject
mailer.from = "name<email address>"
mailer.to = this_to
mailer.htmlbody = this_body
mailer.send
set mailer = nothing
PROBLEM: The process is working fine for most of the email clients, but email body is cutting off for SOME of the clients with domains ending in rr. (road runner) and a few other miscellaneous domains.

Any suggestions or work arounds out there?

I'll assume that you are sending an HTML email. Add some Newline characters throughout your email body. Like after each Table </TD> Else your body is sent as one really long character string without any breaks. Some Systems can't take that much data on a single line. I used to have the same problem and that solved it.