Your replacements file shows that your hr css search was done with the control value AH as target:
Code:
14\Name=CSS Replacements/CSS - hr
14\Find="hr {\n\tborder: 0;\n\tbackground-color: #000000;\n\theight: 4px;\n\twidth: 85%;\n\t}"
14\Replace="hr {\n\tborder: 0;\n\tbackground-color: #000000;\n\theight: 4px;\n\twidth: 85%;\n\t}\nhr.hrsep {\n\tborder: 0;\n\tbackground-color: #000000;\n\theight: 1px;\n\twidth: 4em;\n\tmargin-top: 0.75em;\n\tmargin-bottom: 0.75em;\n\t}"
14\Controls=RX WR DN AH
The target set to AH means all html files. The target should have been AC for all css files.
Please edit that search in your Search Editor and edit the Controls field and snap a screen shot of your target. Perhaps that Controls widget is broken somehow? If you select "All CSS" files the AC control should be set in your saved search not the AH.
What appears after double clicking in that control field in the saved search editor and setting the target to All CSS files then clicking outside the controls to save it?