I believe the mlt xml as clip is not a very well tested/stable feature, you should try to work within the “main” xml directly.
Not sure what effect you’re after but you can add filters to the “Output” track and keyframe it there to apply it to the entire timeline which should basically do the same as applying a filter to the mlt xml. This has always worked and is very stable for me.
I recently reported 2 bugs (and here) with mlt xml that are being fixed (or part of them, I guess it depends on complexity) for the next release. The one with output filters duplication might be connected to your issue here.