I haven't opened the program in a bit, but unless they fixed that issue (which they may have since I last checked lol), whenever you close the program and open it again, all spaces were removed from any inserted code and it's all pushed together. I know I saw a post where a few people including myself commented on this, and if I recall I think Scott said something about checking on this for an update, but not positive on it all as it was a while ago.
I do remember that all white space is basically gone once you close the program and reopen it so if that's the case, and if it hasn't been updated yet to fix that, then don't waste your time trying to fix it.
What I do is put the code into a text editor and save any code I add into a text file so I can always use it over and over and tweak it there and then insert using the HTML Tool, replacing or editing or adding whatever code I need. This way when it removes all the white space I still have the structured code in the text file.
Hope that helps and if that's been fixed .... well then .... nevermind