Other countries have faced similar dilemmas. Part of the reason the Dutch no longer use their historical blue-white-orange tricolor (their flag is red, white and blue) is that it became associated with Nazi collaborator groups during World War II.
Good post for the most part but I'm pretty sure the Dutch don't use orange on their flag because orange dye fades with sun exposure.
I'm sure that was the original reason, but it's kind of a non-issue nowadays with synthetic dyes. (Pre-1994 South Africa didn't seem to have any problems having orange on their flag.)