0.92pre2beta, if you're interested:
http://forum.inkscapecommunity.com/index.php?topic=347.msg2987#msg2987 But the stable 0.92 should be released pretty soon.
Now that I think about it, I think I might havea come across that bug before. Glad to hear it's fixed!
I didn't see any partially transparent strokes in your file. But it's a relatively complex file, and I probably just wasn't looking at the same thing Lazur looked at. That's why I asked you to show me specific objects.
The solution to your problem is using Shift key when you click on the palette, to apply a stroke (or change the color). Lazur happened to discover something else, which could be adding to your confusion. And I know how confusing it can be, with partially transparent strokes. Sometimes it looks for all the world like you have a whole different colored, separate stroke -- and you're like - where did that come from?! Or you know you set a certain color, and it's not showing up!
Were you using transparency on purpose? Inkscape has an annoying default behavior, which one of these days, I'm going to get up enough courage to ask developers to change (fix, imo). Here's a short tutorial/article I wrote to help newbies understand, and have more control:
http://forum.inkscapecommunity.com/index.php?action=articles;sa=view;article=18Or if you are trying to achieve some particular effect, we might be able to suggest ways to do it. Please feel free to describe it or show us an example.