Hello and sorry for the late reply!
Do you by any chance are using post processing effects attached on the Render Camera?
There is currently a limitation where cross-dissolve does not work correctly when camera effects are used. What is basically happening if that is the case, is that the dissolve is taking place from a camera render without post effects, to a camera render with post effects.
Of course this is something I am trying to solve.
Please let me know if that is indeed the case.
Thanks.