I’ve a button that calls a method to change the BorderBrush of some controls, but the color stays the same. I can change the BorderThickness though. BUT If I set the BorderBrush to red and the Background to green, the text cursor turns pink:
private void InvalidateControl(TextBox textBox)
{
textBox.BorderBrush = new SolidColorBrush(Colors.Red);
textBox.Background = Brushes.Green;
}
Yet the actual colors stays the same 
Note: This is a Wpf usercontrol inside a Workspace viewitem.
What you describe sounds very odd (the text cursor in pink bit of it).
In general to be able to control colors you will have to avoid the Smart Client theming.
We have modified the documentation (next version)
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To avoid theming:
When a WinForms UserControl for some reason should not be themed, the following assignment to the UserControl’s Tag property will prevent this UserControl and all inner controls from being themed:
this.Tag = “DoNotThemeMe”;
If using a WPF user control you should instead apply a style. If a style is applied it will not be overwritten by the theming behavior in the Smart Client.
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The general description on theming (but not yet updated with the above) is here -
http://doc.developer.milestonesys.com/html/index.html?base=gettingstarted/intro_theme.html&tree=tree_search.html?search=theme
If you apply a style does it solve the issue?