Why do I get different results when I compare between the same ecoinvent unit and system processes?

The difference probably lies in whether or not you decide to include infrastructure in your calculation setup. The 'Exclude infrastructure processes' option only affects ecoinvent unit processes - ecoinvent system processes include infrastructure by default.
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So in your comparison analysis, if you exclude infrastructure (thus select the box 'Exclude infrastructure processes') the processes will show different impact results. If you deselect that option and calculate again, you should get identical results.