I'm not sure if this is a bug or not but when I try and use separators to customize my toolbar, sometimes they show up as a vertical line but most of the time they just seem to add a little extra space between buttons. One time I got it to show up as a line and then they later changes into space or padding between the buttons. Normally it's hard to get them to show up as a line. I only managed it once.
Let me say, though, that having Accordance for the PC is stupendously wonderful. I used the emulator for years but it was clumsy and eventually grew unstable, at least on my system. I use Bibleworks and Logos as well but much prefer the usability of Accordance.