This is a common issue, I see all the time.
The issue is a combination of having the proper ports forwarded and making sure you have the cert configured correctly.
I struggled with the cert issue for a long time, and I was never able to get it to work by following the deployment guide, but I was Abel to get it to work though a non standard method.
If your ports are all forwarded correctly, but you still get the red triangle saying the phone is partially connected, then you have a cert issue.
You must have a valid domain name for the IP Office for this work at all.
First go to the security section of IP Office and generate a new cert. pay particular attention here. DNS:LAN1, DNS:LAN2, DNS

UBLICIP, URI:SIP:FQND, URI:SIP:LAN1, URI:SIP:LAN2, URI:SIP

UBLICIP
Generate it.
Export it..
Install on all devices.
This still was not enough for me, and this next part is where I went crazy.
Just go the IP Office Webinterface using FireFox.
When the screen comes up asking you to add an exception, don't do it just yet. Choose to view the cert.
From within there you will have the option to export the cert.
Create folder on the Desktop and export the cert.
I took the nuclear approach and exported every version of the cert that I had options for.. PEM, PEM with Chain, PKCS.etc..etc.. Then installed all of them. ( two of them failed because of wrong format ) Does not matter.
Install that on all your devices, and make sure to trust them.
Finally, Equinox start up with no red triangle, and showing presence and System directory.
So essentially, even though you do need to go through the process of creating the cert in IP Office, the one downloaded directly from the IP Office does not work on its own.. I don't know why.
You need to grab the cert from the browser. Install that one... don't just add an exception. Make sure you export it using the browser so you have it handy to send to your iPhone/Android devices as well.
For iPhone, don't forget to trust the cert after installing the profile.
Settings->General->About->CertificateTrustSettings
Hope this helps.