The Ignore Case in Patterns controls whether case is ignored or respected when using all of the above set of filter patterns.
The Ignore Case when Matching Rows controls whether filename case is ignored or respected when the contents of the 2 directories are matched up. For example, when enabled a file "FOO.TXT" would be assumed to match up with a file "foo.txt" in the other directory. When disabled, they would appear as 2 peerless items. This option also causes the folder window to be sorted with a case-insensitive sort.
These options are primarily intended for Windows and Mac users which have case-insensitive filesystems.