Unfortunately, some software packages do use their own 'skinning' engines and therefore do not adhere to the user's settings. In these cases, it may be worth contacting the developer and highlight to them the need for an accessibility mode that turns off the skinning and allows the application to run with the OS' themeing options.
Even if a high-contrast theme for the visually-impaired were created for WindowBlinds, there would still be applications that would, i dare say, stubbornly refuse to comply.