I am trying to access the Optimize Drives application - but nothing happens when I start it from the start screen or from the Drive Tools tab in Explorer.
I did tried to analyze the 250GB system partition and it worked (less than 1% fragmentation), but nothing happened on the second logical partition (750GB).
Please go ahead and post a screenshot of the command prompt showing what it did when you ran chkdsk on the second logical partition (750GB). It may take a bit for it to display results.