According to the official Paizo FAQ, humans will always end up with a minimum of 2 skill points per level.
"Human: For a low-Int human character, is the minimum number of skill ranks per level 1 or 2?
It's 1, but you add your human bonus rank at the end, so you end up with 2 ranks total. For example, a human fighter 1 with Int 6 would start with 2 ranks, add the –2 from the Int penalty (for a total of 0 ranks), apply the "minimum 1" rule (for an adjusted total of 1 rank), then add the 1 human rank (for a total of 2 ranks). In other words, a human should end up with more skill ranks than an otherwise-equivalent character of a different race."
I was able to fix it by adding XTRASKILLPTSPERLVL:1 to cr_races.lst line 12 and removing BONUS:SKILLPOINTS|NUMBER|1 from cr_abilities_race.lst line 147.
Also, I don't think it has any effect, but the IntegerKey for XTRASKILLPTSPERLVL is SKILL_POINTS_PER_LEVEL which is assigned the constant for "AC_CHECK". See IntegerKey.java line 114. Looks like a cut-n-paste error.
The Low Intelligence portion is now fixed in the main development line (At revision: 23634). However, I'll push this over to the code team to look into your find.