We are using Media 100HD. This is the first project having this issue also. When adding titles to a program then exporting using self-contained or by reference the screen brightens about 10% during the length of the title. This does not happen when watching it in real-time or exporting with other methods (h.264, animation, etc...) Can anyone shed some light or has anyone experienced this as well?
You have a codec mismatch on your timeline. You have acquired your video material in one codec (e.g. DV, ProRes,...), and you have rendered into a different codec (e.g. Media 100 i, Media 100 HD). The Media 100 codecs use a different colorspace when watched in RGB (QuickTime) than the Apple codecs, although they look identical when watched in their source YCrCb format via Media 100. If you have mixed codecs in your timeline you should do a full QuickTime export into a codec of your choice. Or make sure that you render into the same codec as you acquired.
Note, that you also can get into a field order mismatch. E.g. DV PAL is Lower field first, while most of the other PAL codecs are upper field first. If you export a timeline by reference with e.g. DV and ProRes clips you will have either the one or other clips with a wrong field order. Media 100 does handle all this in the background when working inside the app.