I'm having the same issue with my paladin main character (level 13, loaded savegame that was started before v3.00.929 PX1-Steam). Paladin MC has maxed-out (4/4) relevant favored dispositions, though I understand only the first 3 levels of each disposition granted Faith and Conviction bonuses. Also no ranks in disfavored dispositions.
Before the 3.00 beta patch, Faith and Conviction maxed out at:
+11 deflection (5 base + 6 from dispositions)
+22 fort/ref/will (10 base + 12 from dispositions)
Under the 3.00 beta patch notes, the base bonuses for Faith and Conviction have been reduced to +4 deflection, +8 fort/ref/will.
As such, a paladin MC with maxed-out favored dispositions (and no disfavored dispositions) under the 3.00 beta patch should be:
+10 deflection (4 base + 6 from dispositions)
+20 fort/ref/will (8 base + 12 from dispositions)
However, under the 3.00 beta patch, my paladin MC shows Faith and Conviction bonuses of:
+8.8 deflection (4 base +1 every 5 levels after 0) (note: rounds down to +8 when calculating total deflection)
+17.6 fort/ref/will (8 base +2 every 5 levels after 0) (note: rounds down to +17 when calculating total fort/ref/will)
There are several issues here.
First, why are we even getting decimal values? Whether the paladin is the MC or Pallegina, there should never be decimal values.
Second, the Faith and Conviction values aren't even being calculated correctly. If the deflection bonus should be (4 base + 1 every 5 levels), then a level 13 paladin NPC should have a total +6 deflection bonus.
Third, and most importantly, it appears the Faith and Conviction bonuses for a paladin MC aren't getting properly calculated based on disposition. It's possible that it's now using the NPC calculation (bonuses calculated by level instead of by disposition) for the MC as well, though nothing in the patch notes indicates that should be the case.
On a related note, did Deep Faith get nerfed somewhere along the line? It used to provide a flat +2 deflection and +5 fort/ref/will bonus to Faith and Conviction. It's now +2 deflection and +3 fort/ref/will bonus.