I've been dealing with the same issue and I found that when I went into the Advanced menu and selected to enable the usage rights, it said that the file already had them. I did a "save a copy" which removed the rights and then re-issued the rights with the Advanced menu. The file seems to be functioning fine in Reader, I was able to enter data into the fields, close the file and it was still there when I reopened it.
Using Acrobat Pro 8 and Reader 8