It works fine with the 2- 9V batteries in series (TIP31 does get a little hot). When I connect three 6 Vs in series the TIP31 and LM358 fry.
Sounds very much like a problem with the circuit.
Two small 9V batteries can't supply enough current to do much damage, but I guess your three 6V batteries can. If the circuit is supposed to operate from 18V, then using three 6V batteries should not cause the semiconductors to lose their smoke!
Also I have to ask, because this mistake has tripped people up in this forum in the past: You know that when you measure battery load current, you disconnect one wire from the battery and put the meter across the gap? You don't connect it straight across the battery.
I ask this because you say that you "need about half that current" which is not a meaningful thing to say in this case. The circuit should draw the amount of current it needs; you shouldn't be adding resistors to change the current drawn by the circuit.
We like to help, but we need MUCH more information.
What frequency are you operating the circuit at? What are the details of the transformer?
The most important thing for you to do is:
POST THE CIRCUIT!
If it's hand-drawn, scan it. That's fine, it doesn't need to be beautiful.
Also a photograph could be useful.