What is your Shotcut version (see Help > About Shotcut)? Is it 32-bit?
Can you repeat the problem? If so, what are the steps?
I’m not entirely sure if this is a bug or what is supposed to happen, but I have on track 1 (bottom track) a clip of a person, track 2 a black colour clip with an opacity filter that goes from 0 to 100 over the course of it’s clip, and on track 3 (top track) a clip of butterflies that I have Chroma key: Simple filtered to get rid of it’s green screen. when the clip runs however, the opacity filter for the black colour clip does as intended to increase it’s visibility (and thus provide a fade out/to black effect) but for some unexpected reason, also covers the butterflies which are on the track above it. To my understanding, this shouldn’t happen, but rather the clips on track one (of the person) should be covered by the clip on track 2 (black box) with the butterflies layered on-top of said black box. (I do realise now that I have written this out that I can use the fade out effect for Track 1, but this opacity filter seems to be bugged/conflicting with the chroma key: simple filter on the track above it)
I have blurred the persons face for privacy reasons
Edit: the track at the very bottom with a white box was my attempt at fixing the issue by assuming that the butterflies green screen needed a background colour other than black to stay at full colour in the video. However it didn’t work.
I had changed the order of the track around a small bit (can’t remember what one’s and where to) so that bug might be a major contributor to the issue. Also I realise I typed out my tracks a bit incorrectly and will fix that here: V1 (bottom track) - completely white image, V2 - image of person, V3 - completely black image with 1 filter: Opacity (starting at 0 at beginning of clip, ending at 100 at end of clip), and V4 (top track) - clip of butterflies on a green screen that I used 1 filter to erase: Chroma Key Simple (30% focus).
Now that you mention a known bug regarding the reorder of tracks, this would also explain why I’m having a near identical issue with another video I am working on where V2 (lower track) is displaying over V6 (higher track). So I do believe this is a case of the bug.