Since 21.9 you have added a TOD waypoint before which you cannot descend from the cruise without triggering the error message?
Not quite, perhaps I can explain the restriction differently; it has always been there, but wasn't working correctly:
There can only be only one Top of Climb (TOC) and one Top of Descent (TOD) position, both initially at the assigned cruise altitude.
On the way up to TOC there can be several steps; normally PF3 will set the first waypoint to the cruise altitude and assign appropriate steps.
Similarly, PF3 will assign a number of steps down from TOD, generally to the final approach altitude.
If you need to set specific waypoint altitudes then you need to ensure that they increase towards TOC, and decrease after TOD.
The updated version of PF3 simply enforces this restriction, and won't allow you to save a 'bad' profile.
Hope this helps,
Martin