When you CTRL + Click to select multiple rules (selected rules have the row highlighted) and then delete, it deletes different rules than those selected. If you select multiple rules by Mouse Down + Drag it deletes the correct rules. CTRL + Click is the most convenient method to select rules, this type of selection and deletion should be properly supported

Update: 1.6.7 fixed Ctrl click delete, but now it deletes the wrong rules for any selection, this PR needs to be included in new release to fix rule delete: #1252