We also have the "odd" indications when we installed Phase 4. The problem we have with the ILS is that the aircraft does not fly down the centre line, but slightly off to one side.
When changing from P3 to P4 there were a lot of wiring changes, GPS and AHRS were involved, it is worth rechecking these changes. Are you basic 4 axis or enhanced?
Phase 5 does fix some of these problems, introduces some new features and also some new problems.
We also have numerous trim fail warnings, usually pitch or roll, these reset by reselecting the A/P channel, another irritating issue.