Yep...something strange is happening....and shouldn't (at least not normally)
The only way to track it is to have a PDF printout from before the update, and compare it line-by-line to a PDF printout after the update, so that you can see exactly what changed (and shouldn't have).
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But once the update has already happened, it's hard to know where the foul-up was occurring. So, on the file that has changed, you'd need to go thru the entire tax interview Q&A again editing every form to see if it changes back to the taxes owed/refund you expected initially.
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OR...worst case.
1) Save a PDF of the updated filing forms....and print out.
2) Then, start a NEW file for the 3rd time (I know...AHHHHH..Noooo!)....make sure you do a SAVE-AS to a specifically-named different file name soon after you start. Then when you get to the point where your taxes-owed was back to what you saw originally...save it and print out another PDF filing copy.
3) Then compare the filing copies for #1 to #2 and see what line(s) have changed, and track down what's getting screwed up that way.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
