All the ports in use could mean 1 of 3 things;
A. Ports in use by callers (not common in a small system like the CIX 40)
B. Hackers
C. Ports stuck in a loop (most common)

A and B should be obvious to the customer because the CO trunks would also be in use.

Unfortunately even through the CIX 40 is pretty much plug and play, the default settings can create loops in the voicemail when the caller hangs up.
On every system I install, I change these settings from the default to prevent voicemail loops.
- Trunk disconnect supervision enabled
- Change default operator extension (0 doesn't ring anywhere in the PBX)
- Hang up after recording in general mailbox