I was having the same problem. The “… [read more]” was showing up in the middle of some excerpts, not the end.
I discovered after much trial and error that if, in the Advanced Excerpt Options section, I went to the Keep Markup section and UNchecked the boxes for the following two html tags
[em]
and
[strong]
…the plugin placed the “… [read more]” at the end of the excerpt.
Unfortunately, I was hoping to keep the em and strong tags, which was part of the point of using a plugin (to keep the styling), but something’s better than nothing!