Dear Dimitri,
Helmut has already given a very comprehensive explanation for some of the causes for differences in results. The change to spm_get_ons.m you mentioned was added in r3677, dated Jan 14, 2010. You should see a similar effect if you run your analysis in unmodified SPM8 r3042 and decrease the "Microtime onset" setting in your model specification batch by one (unless it already has a value of one).
The section 'stats.results' in the spm_defaults.m file is responsible for results display. The values there only determine the default appearance of results reports. Some of these settings disappeared from spm_defaults.m and have moved into the batch configuration files. They are inserted automatically when you create a new batch with a results report module. When loading an existing batch, the values will be read from the batch file. None of these settings in 'stats.results' should have an impact on model estimation.
Best,
Volkmar
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