Retirement tax questions

Either this just happens in a small number of cases each year or most people never think to check it manually, after all that is why we use tax preparation s/w.  I do my sister's simple taxes each year along with my own.  Her income is 1099-R and social security.  She always has $600 taken out of her retirement, "just in case" she had taxes to pay.  Each year she gets it back, as her income is too small to pay any taxes.  This year TT said she was getting nothing back, so that was an obvious red flag.  I investigated and found that the $600 had been accepted from the input form but was never transferred to the 1040 form.  I had to do a manual override to get it to work correctly.  I would like to know which piece of s/w does this transfer between forms and what is its latest version.  TT always says it checks for s/w updates and I always install them when it says there are new ones, but I would like to check this out manually to confirm it.  As I said, this has worked fine for the past 5 years, and I am using the same computer, and still getting my download from Amazon, and then running the updates.  But it looks like some people have had this problem in the years when I did not have it.  This sounds like when I get an update from my backup s/w vendor which says that a few users with ...  have had problems backing up a particular type of file and they finally determined why it was happening.  TT needs to look into these corner case problems more seriously.