If you are having an issue with new lines seemingly being stripped out from your comments, item text or anywhere else, the solution may be very easy to remedy.

 

If you look at the first screen shot you can see we've entered a couple new lines, and in the second screen shot you can see all the text is thrown onto one line when saved/displayed.

 

The reason for this is simple: the WYSIWYG editor inserts <div> tags for new line lines, and you probably do not have the <div> tag as part of your "allowed HTML tags" configuration.

 

If you go to the tools page, scroll to the "security settings" area to find a tool reading "manage allowed HTML tags" (admin tool 200). Odds are the <div> tag is not a part of this list, so add it now, like in the third screen shot.

 

When you go back to look at the comment, you will see that the new lines *still* are missing and the text appears all thrown together. This is because comment & item output text/HTML are cached to limit excessive text processing. If you edit the comment and simply save it again, all will be fixed. If you have lots of comments or items which are effected by this quirk and manually editing and saving each of them is not a realistic solution, you should use two additional admin tools: "cache text for all posts" (admin tool 089) and "cache text for all items" (admin tool 090) - both of which are located in the "maintenance" area.