Any reason why the technique of making pasta bake without pre-boiling would cause me violent stomach upset?

It doesn't really make any sense how this could possibly be related, and for that reason I don't rule out some other factor being at play, but the correlation has been pretty evident on all 3 occasions when I tried to do this and the absence of the same effects when I don't do this and instead do pre-boil the pasta all seem to point it being the relevant variable.

Assuming the no-pre-boiling somehow is responsible, the obvious solution to the problem is to just stop doing that and indeed I have for fear of a repeat of the horrible experience, but it's just that the ease and efficiency of the method is so appealing and I would like to try it again, but I also really don't want to gamble on that unless I can be pretty well assured that the results were unrelated to the lack of a pre-boil or if that actually is a plausible cause, I'd like to learn by what mechanism this could possibly play a role and why it doesn't bother most people.