As for being haunted by WordPerfect for ever, I have no idea as I never used it. I loved Word 5.1a … after that it was downhill all the way … and the only Microsoft thing I have on this is a copy of instant messenger needed to set up my MSN account. I use Adium for all chats.
Yes, Mellel has a steep learning curve, whereas Nisus is very Mac-like and intuitive. There are still those who complain, though. I moved over from Mellel, not because of the interface, in fact, but because at that time it was a lot of hassle with Chinese which I’m exchanging all the time with others. Soon after I found that, I found an embryonic word processor called Okito Composer which showed promise. After a year or two the developer, Charles Jolley, sold it to Nisus who were still trying to develop a replacement for the OS-9 Nisus, and it became the foundation of Nisus Writer. I moved on to Nisus Writer Pro when that was developed.
I haven’t used Nisus Writer Express for two or three years now, and can’t remember what the differences are, but if you’re into a book that’s going to need a table of contents and an index, and you want cross-referencing then NWP is definitely the one. It uses RTF as its native format though it can export to .doc. And I haven’t yet met anything that I would prefer to use.
As for your last question, have a document open in Scrivener, then choose the menu, down the bottom is which gives you an option . It’ll come up with a warning that the change is irreversible, so perhaps try it on a duplicate of one of your files in the binder — hint, highlight the file in the binder and press Cmd-D. It will convert the file to the format that is specified as default in the preferences … see if that removes any gremlins.
Another possibility is to open one of them in Nisus Writer (Pro), or copy and paste into a new Nisus Writer document, and then from the menu, I think it is, choose . That might show you any hidden characters that have been left behind in the transfer from WP. You can delete them, save the file back out as RTF and then bring that back into Scrivener.
I believe there has been talk of “Show Invisibles” coming in version 2 of Scrivener, but I’m not sure.