Tyler,
"What can I learn from this?"
Does your stove and your cook pot form a "seal" where they meet? If they do you could be over pressurizing the stove's jets as everything heats up.
Can you increase the circumference of your windscreen so that the gap between the cook pot and the windscreen is larger?
Some of the bottle stoves use raised dimples where the cook pot rests on top of the stove. Does your stove have these raised dimples? If not try a burn with a "triangle" of SS wire between your cook pot and your stove. .020" or .030" SS wire should be a large enough diameter for a trial run. This may help in reducing some of the pressure at the jets.
If it does then you have to decide if you want to "dimple" the top of your stove. ;-?
In the picture below there is an example of what I am describing.

Look closely at the top left of the stove in the picture for an example of the dimpled top on a bottle stove. There are three dimples spaced equally around the top where the cook pot rests.
Note:
The stove in the picture is made from a 6 oz bottle but the principle can be applied to a 12 oz bottle stove.
I would think that you could accomplish the same thing by using a round file and "cutting" 3 reverse dimples into the stove's top rim being careful not to cut them completely through the coped rim. ;-?
This modification would be irreversible!
Make each test burn changing only one thing at a time.
Party On,
Newton