Will this charger fully charge 600 mAH 9 volt batteries? My current charger can only charge to 80%.

It should. If your charger can charge your 200 ma batteries ok but not your 600 ma battery, I would suspect you battery. This charger will keep charging until battery is full. This works great for the Imedion true 9.6 volt battery (Taiwan not China).I would rather have a battery stay at 9 volts a lot longer then have more current at lower voltage that a rated 600 ma battery has. From what I’ve seen the 600mah dip to 6 volts in a straight line more so than a name brand 200 ma batteries. At lot of junk 600 ma batteries are out there. A higher current battery generally has a much shorter life. To date I have not seen one China made battery deliver rated output.

Manual says plug in wall adapter first, then plug unit, then install battery. Is this order absolutely necessary? If so, why?

No specific order is necessary. Probably the best order is issued by the manufacturer because some electric induction peak while a charged battery is in place. I didn't experience any trouble using this charguer for years with any kind of rechargeable 9V battery.

A red light blinks next to a new powerex 9v. battery. i lost the manual. does that indicate a dead battery? others charge fine. thanks.

It's been a few years since I used that charger, but if I remember correctly a blinking red light indicates that a battery is not able to take a charge. I encountered the blinking light even with newer batteries that I used only a few times, so my impression was that unless you take a battery through a full charge discharge cycle (that is, not charge a battery when it still has a good amount of charge left), the charger would for some reason think that something was wrong with the battery. I could be wrong. But that was my impression that is why I just stopped using the charger – it always seem to erroneously tell me that a battery could not take a charge! It appears that nothing has changed, and I really haven't found a decent 9 V charger, so I've used mainly alkalines for all of my nine volt equipment. Sorry you may possibly be experiencing the same frustration...

Can you plug the charger directly into the wall or do you have to use the AC adaptor plug in?

The charger has no built-in prongs that would go directly into an outlet so it does require a plug in cord. (This is the church secretary answering--not our tech--so I hope I described it correctly.)