Hello amit,
Regarding your above post, I have followed those instructions exactly in my cluster besides the fact that I called my SYSTEM_DOMAIN "sysdomain" to make it more easily searchable in logs later (I have had to read a lot of log files to debug errors. "sys" is not a good string to grep for as it truns up too many times...)

My stub configuration is as such:
properties:
domain: 10.60.18.186.xip.io
system_domain: sysdomain.10.60.18.186.xip.io
system_domain_organization: sysdomainorg.10.60.18.186.xip.io
app_domains:
- appsdomain.10.60.18.186.xip.io

However, the problem looks like a problem in the instructions.
When I follow your new instructions I immeditaly get a 404 which I did not get beforehand:
ubuntu(a)cf-installer:~/cloudfoundry-stubs$ cf api api.sysdomain.api.10.60.18.186.xip.io --skip-ssl-validation
Setting api endpoint to api.sysdomain.api.10.60.18.186.xip.io...
FAILED
Server error, status code: 404, error code: 0, message:

What more I have read the instructions on using the API which are linked from in your documentation ( http://docs.cloudfoundry.org/cf-cli/getting-started.html and https://github.com/cloudfoundry/cli ). They do not give explicit instructions about which node is the api node, but when I look at the example, it says nothing about accessing it through the system domain.
Also when I used "cf api api.10.60.18.186.xip.io" on the global domain (as in the doc example) I did not get a 404
Please copy-paste above, to see that there is no 404 on the original cli command.

So It does not seem plausible that the problem is as you describe it.