With panchromatic film, the window colour is not so important. Most of my medium format cameras rely on the red window and two of them have no cover for it. I do not experience any problems with fogging on the film.
What film are you using? Having asked that, I have used Kodak, Ilford, Fuji, Adox and Efke films with no problems.
The backing paper is thick enough to stop light - if it was not you would have numbers and things printed onto the film as well as those stripes. I would suggest that you have more problems than just a dodgy interlock with your roll-film backs and there is light leakage from elsewhere, not from the red window.