They are not temperamental at all when connected to the correct chimney.
First, I'm assuming the baffle plate is designed as shown in the Baffle thread in the Fisher section.
The rear of the plate needs to be setting on the rear brick retainers and the front angled upwards toward the low bend on the top.
You should have a 6 inch diameter chimney flue and preferably insulated for baffle that size.
Second, are you trying to heat more than 1000 square feet?
The smoke space above baffle plate where smoke exits must be no smaller than 28.26 square inches. If you're tying to connect the Baby Bear to a larger diameter chimney, the smoke space must be at least equal to the square inch area of the flue to the top. The amount of resistance in the system determines final baffle adjustment. Elbows, connector pipe, spark screen, and damper (as well as baffle) all add resistance to slow draft created by chimney. The more resistance, the larger the smoke space required to allow more heat to escape. The minimum smoke space works good with a top vent, no elbow, straight 6 inch connector pipe into a 6 inch insulated chimney. My test chimney was three 3 foot insulated chimney sections over a 8 foot indoor ceiling with single wall connector pipe. This is the only chimney that may require any additional resistance from a flue damper to slow velocity.
You didn't mention if you're using a flue damper. We need the flue diameter and height.
The intake should never be opened fully. Only spin it a few turns when starting. As fire catches, close down to 1 to 1 1/2 turns. 1/2 to 1 turn is common for normal heat output.
Is this a rear, top or side vent??
Baby Bear is the most susceptible to flutter than all the other models. The small firebox puts the intake opening very close to the fire. The flutter is a fast type of puffing not to be confused with the slower chugging you will get when the exhaust gasses cool and slow to the point of letting colder heavier air into the chimney. It sounds like your flue is too big for the stove and the rising gasses drop down allowing oxygen into the flue. As the rising gasses overcome the drop and rise again, this repeats until the air slugs make it down to the stove. This oxygen puffs back through the intake. In extreme cases with other problems such as mechanical exhaust fans in the building, or stack effect from heat rising in the building faster than rising gasses up the chimney, you get exhaust reversal which is probably what filled the house with smoke.
Tell your wife the last thing to blame is the stove.
#1 is the chimney, then system resistance, baffle adjustment, mechanical blowers or other appliances venting indoor air outside, fuel, operator error.
Thanks, all good info. Esp hellful is your advice about adjusting the damper. I was opening too far, then closing too much all at once.
