Turning off Preferences / Toolbars / Appearance / Use Office 2003-style for toolbars will probably solve both your problems.
I already had that option off. Notice the bright divider :\
Not sure if there is an option in Windows that I can adjust... never looked into it.
When the option is off, the separators come from your Windows theme.
Thanks for that Leo.
I went hunting and found the option. The 3d Objects seems to control this divider. But there are a few problems when changing this.
Changing the 3d Object to something like black, seems like it's going to change some windows that could change drastically. At first I think I was ok and couldn't find any windows that would be affected. Until I started making screenshots. The Dopus viewer's bottom toolbar is now in all black and when doing a Save, the dialog box is now all black. Now I'm also finding a lot of other open/save dialog windows that are affected by this radical change.
I'd still love if Dopus could overwrite this 3d Object setting with it's own in some way. Actually even controlling borders would be great as well.
You've set both the background/border color ("Color 1" in the Windows control panel) and the text color ("Color" in the Windows control panel) to black, which is why you've ended up with black-on-black in places.
We might add a way to override the separator colors in a future version. We assumed people would want Opus to look consistent with the rest of their desktop but that's obviously not always the case. 
I noticed that after I already made the screenshots and didn't want to redo them 
I changed the font color and it didn't help but hurt other windows... like buttons with light colors now had light fonts
Doesn't matter about the font though.. I don't want black windows. No idea why a background color of a window would be affected by a 3d object adjustment really. Changing this also hurt my Windows Live Mail client. Now I can't get it back... no idea what the default color was (I thought it was white but seems wrong).
If it changes in the future, great. I'd prefer not to have to mess with the Windows themes. Probably why I gave up on them last time and just added spacers.
Thanks for your time Leo
On Win7 the default is the bottom-left color in the chooser that pops up (240,240,240).
Actually, I thought that too but it's not, that bottom left color changes with what you had last picked and then on each new color pick, the other colors start moving around. Thanks for the RGB values.
We've done this for the next update:
Yayyy!! Awesome, I can use a dark theme then 
Cant wait on the next beta 
Freakin Sweet! Look how hot that looks
I can now also change the font color in one spot instead of each button
Thanks!! 
I'd also love to be able to theme the scrollbars and toolbar arrows separately.
Yes
Great, thanks! 
When is the version of Dopus that includes this gonna be released? (Or has it already and I've missed it in settings?)
You can grab the latest beta version (at the time I type this) from here: Directory Opus 10.2.0.4 (beta)
Is there also some way to do the same to the menu borders, and the "whatchamacallit" (for lack of a better term 
. See attachment)
Turn on Preferences / Toolbars / Appearance / Use Office 2003-style for toolbars and you get more control over the menu colors as everything will then be custom-drawn instead of using your Windows visual style.
I had that set originally, but then I was having problems finding how to change the background of the menu from solid white. The sidebar of the menu would change, but I couldn't get the menu background itself to change.
Oh, that's true. 
From your Firefox/Opus screenshot, it looks like Firefox is using a completely different visual style to draw its menus. Have you installed some kind of custom theme for Firefox or something? Or are you using something like WindowBlinds set to use different visual styles with different programs?