> Serious question: why is it so hard for them to find the root cause of these issues?

Biology is hard. Humans are really, really variable. Look through the comments on this page - you'll find people who couldn't keep down one bottle, or who love the bottles but can't stand the powder, or who have had zero issues, or who find the entire idea disgusting.

And these reactions may also change over time. Medical science can only really draw firm results from large-scale tests involving highly-controlled groups - and even if Soylent were able to run those kinds of tests and optimized for the most universal solution, the end result would probably still disagree with someone.