Someone had a similar problem a little while back. It wasn't a strikethrough, IIRC the grid lines in the issues window were display ing wrong and were going through the issues (as well as above and below as they're supposed to). If this is the problem then its just a display problem, the issues cleaner should still work fine, there certainly isn't any function in CCleaner for striking through issues for any reason.
Unfortunately I can't find the thread where this problem occurred, maybe someone else will remember what was causing it