Well, running passive front stage with tweet/mid in two different locations is definitely NOT going to play well with TA.
For TA to work properly, each speaker needs to be ran on its own channel. Since you're running passive, you actually have 4 speakers in 4 separate spots with only 2 channels. This is probably why you see funny distances since the HU "thinks" the front stage is only 1 full range speaker..
The P99 was designed to run an active 3-way front stage and subs, on all individual channels. It has the capability to do all the crossovers for each speaker, so using passives is pointless.
Im only using 6 of the available 8 channels. Im only running a two way front stage and no rear fill.
If I were you I would get a 4ch and run the front stage active, just leave the rears disconnected for now, re-do the Auto TA and see how you like it. The TA would yield much better results like this.
EDIT: I know its more work to run separate speaker wires for each speaker, but thats how it was designed to be ran. When I installed my system over 6 years ago, Im glad I ran extra speaker wire from the trunk to the front, just in case I decided to run active one day