I don't know if it's related, but I had an issue with one of the earlier builds where an animation that caused a character to 'flash' would actually make their sprite go black instead of white - or something along those lines (been a while). Strangely enough, this only happened on particular versions of a particular browser. I believe that issue was fixed, so it may be that something as simple as updating your project will solve the issue.
If you're using the Steam version, you should be getting updates automatically. But this will only affect new projects - it won't go back and update those you've already created. Easiest way to do this is to create a new project, then go in and copy all the files within the js folder (except plugins.js and the plugins folder itself) from the new project and paste them over the same-named files in your old project. Might be worth taking a back up of the js folder in your existing project first, just in case. And afterwards, you should probably check that all the plugins you have are compatible with the 1.2.0 build of MV.
I can't be sure that's going to fix your problem. It's just the first thing I'd do if I had that issue.