The Phenomenon is:
Since the speakers are installed in the parcel shelf, remember its firing in both the directions one inside the cabin and the other inside the trunk (opposite phase).
Now about the sub; since it is located in the trunk, the bass from the sub is interacting directly with reverse firing of the rear speaker.
Now we can easily match the phase of the speaker firing in the trunk with the sub, but we are not sitting in the trunk are we?
Now if we correct the phase of the sub with the rear speaker (which will be the back side of the speaker in phase with the sub) will sound right and in phase.
But the moment we turn on the front speakers, the phase of the sub will totally be the opposite for the front speakers.
The scenario will be, the front speakers and the rear speakers will be phased correctly...!!!! BUT...!! the sub will not be phased correctly. Either the sub will be in right phase with the rear speakers or the sub will only be in correct phase with the front speakers.... But not both.
Reason:
For correct phasing of rear speaker with sub... we have to adjust the phase of the sub with the opposite firing (reverse phase) of the rear speaker.
For front speakers we have to adjust the phase of the sub with the front firing (normal phase) of the front speaker.
In Short:
In the above mentioned scenario, we can only phase the sub either with the front speaker (but the phase will not be correct for the rear speaker) OR we can only phase the sub correctly with the rear speakers ( but phase will not be correct for the front speakers)