Do I still suffer a -4 penalty for firing into melee if I'm flanking an enemy with someone else and using Point Blank Master. Assuming I don't have Precise Shot of course
Yes, Point Blank Master only does exactly what it says it does. It doesn't take away those negatives.
Yes, you still take the normal -4 penalty. Note that you also don't gain a bonus for flanking (as it only applies to melee attacks) and you also don't count as threatening to grant flanking bonuses to others.