Answer
You will need to update your ISA configuration with the proper rules & exceptions (specific to your site & your configured agent port) for it to work correctly with Kaseya Agents. If you are not able to do this, please visit the following ISA Support webpage for information & support from Microsoft regarding this particular product:
http://www.microsoft.com/forefront/edgesecurity/isaserver/en/us/support-options.aspx (note the MSFT discontinued announcement in this)
Further options from this are noted here too - http://blogs.technet.com/b/server-cloud/archive/2012/09/12/important-changes-to-forefront-product-roadmaps.aspx
Also, you may contact training@kaseya.com to setup time w/ Kaseya Professional Services to do this as well.
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The following is a temporary workaround to at least have your agents check-in, though other components of the Kaseya Agents may not work (ie.: Remote Control):
On the Active Directory Side, create or select an AD account that is a member of the Administrators group.
On the ISA software side, configure this same AD account to have full ISA-internet priveleges.
On the Kaseya Agent side, within the Agent > Configure Agents > Set Credential page, set the credential for these particular agents in this environment to reflect the username, password, and domain of this particular AD account.