Removed line breaks=random font resizing

Hi there, I have a large mobi file which is an omnibus of several books. The first book has a line break between each paragraph, but the rest of the file is perfect. So I ran it through calibre to remove the line breaks - just 'remove lines from between each paragraph' under 'look and feel' - and the line breaks disappear perfectly but the font in other parts of the whole file have randomly shrunk.

I've done this three times and can't work out how to stop the font from shrinking. Again, it's not the font of the entire file, just big chunks of apparently random text.

Can anyone help me?