Well without more specifics I can't really help. I've never seen some of the issues you bring up; other things that "look wrong" to you are actually not wrong. Let me tackle the ones I can without having more info:
Rings have 0 value in the generate treasure app (bug, fixable) -- I can't see this problem anywhere, either in the treasure generator or in the character editor/purchase screen. They all have gp values.
Rods have 0 value in the generate treasure app (bug, fixable) -- ditto. (this is why I need more detail)
BAB's are listed in reverse order (ie, +2/+7) (bug, fixable?) -- Again, I'm going through both monster stats and character stats and am not seeing this.
Weapon Focus isn't taken into account for Attack Bonuses in the stat block -- again, it's working for me -- under what conditions doesn't it work for you?
When trying to create a group of monsters (Warband, 4d8), it creates a whole freaking tribe. (bug, fixable?) -- I'm not seeing where you're generating this at. I can find something called Warband under Generate Table - Hobgoblin - Warband, but am not sure if this is what you're referring to.
No such thing as Mithral Shirt +2 or Large Mithral Shield +1? -- Fluid (as contracted) built the stuff in the DMG. Show me where you can generate those things on the DMG treasure tables. Now, you can go into the house rules area and build these things to your heart's content.
Can't give my PC wands (Rogue with 13 ranks in Use Magical Device) --- none listed. -- wands are "built" based on class/level/spell selections as described in the DMG. Use the "New" button on the purchase screen to see the ways to combine items like this. Same deal with potions and scrolls, btw. This allows you to add new spells in the house rules and then you'll be able to build wands, scrolls, and potions from them.
Does not calculate bonus languages correctly when generating a PC/NPC -- I need details, in my experience it's working ok. Remember there are three ways to get languages (automatic, bonus based on high INT and a list of languages per your race, and spending skill points).
Does not calculate skill points correctly (forgets to add in INT bonus every level including 1st) -- You're encountering a frustrating part of the D&D rules -- INT additions to base scores do not retroactively adjust skill points. In order to hand-enter scores, go to the Roll Stats screen, select the last method called User Entered, and then look way to the right --- you'll see all of the scores are set to 8 and you can user-enter adjustments there that WILL be applied retroactively. But adjustments in that center column (User Adjusted) are not. Agreed, this takes some getting used to.
Does not calculate HP's correctly (forgets to add CON bonus every level) -- more detail needed, I haven't seen this happening.
Incorrectly lists Dwarves inherent magical resistance as +2 reflex save vs spells. PHB (p.15) clearly lists this as +2 save vs Spells & spell-like effects. -- you're right, this is incorrect.
Can't find any support on their website for this thing -- their support is on their message boards. Scott and Eric were in on a Saturday night helping out with things just this weekend. Sorry you can't seem to get through, if you can give me more details like maybe an error message I can take it there and see if it can get fixed.
Other items -- either your opinion, which while certainly valid doesn't mean they "have to change" by any means; or they're items that I myself cannot address.
Finally I should add -- I do know the feeling of not liking software that others are touting as great. PC Gen, after all, just never did it for me -- so much so that I actually preferred to roll characters by hand than to use it. This just might be the same situation with you and eTools.
