I haven’t used this editor before, however, wrapping block of text in paragraph tags is how you put text on the page symantically. <p> </p> tells me that you hit the enter key twice, and they use a space for a place holder. So there is no ‘problem’ with the editor.
You may want to loot at FCK documentation or their forum. I don’t know FCK that much but it’s the same case in TinyMCE editor - <p> tags are enabled by default, which means that all text is wrapped in <p> tags (or <h1>, <h2>, etc. tags) so that there is no loose text outside block tags. This is the preferred and semantic way of coding text. TinyMCE can be configured not to use <p> tags and issue normal <br> on each newline - it’s very likely FCK Editor has a similar setting.