ISSUE:

When you take a Potion from the Creative Menu brewing tab, its numeric value is larger than it should be. The bits that don't have to do with the potion effect requirements are all set to 1.

This doesn't seem to affect using the Potions, but since some of the bits set to 1 control whether you can add more ingredients, you can do some odd brewings.

For example, try taking a 3-minute Potion of Fire Resistance from the Creative Menu, putting it in a Brewing Stand, and adding a Ghast Tear. It will brew into a 22-second Potion of Regen II.

LIKELY CAUSE & FIX:

I took a look at (MCP)ItemPotion.getSubItems(), which generates the set of Potion items for the brewing tab. Currently it loops through the possible values 0 - 32767, adding values that create potions to a List indexed by the potion effect. This means that, if more than one potion value produces the same effect, the list will end up with the largest potion value for that particular effect - hence all the "don't-care" bits are set.

A quick fix? Try looping from 32767 to 0 so you get the smallest potion value for each effect. Note that this may cause other problems if some bits aren't set, so it'll take some checking.

EDIT:
I've attached a piece of code for you to try in (MCP)ItemPotion.getSubItems(). It will account for missing Healing/Harming potions and use the smallest value for each potion effect.