The auto formatting of source gets confused with some constructs and has procedure, functions and begin/end statement indented incorrectly. On the attached file, see the indenting for:
procedure SetPopProportions; (final end; is incorrectly indented)
procedure EnterTransMatrix; (indented incorrectly as a result)
The formatter has issues with some files, this is correct. I can see some problems with the file you attached. In particular, it is clear that there are cases when the indentation loses one level incorrectly.
For the moment I can't do much more than confirm the problem.