Yes, come to the dark side.
Ok, jokes aside, uploading a small sample would be helpful for us to try to see and get rid of those issues. Especially if you're not familiar with Avisynth, we could send you a script to take care of those things so that you just run it and then forget about it. You can even open Avisynth Scripts in VirtualDub (since that's what you're familiar with) and encode from there, it's totally fine.
p.s for what it's worth, I've been using SpotLess() in some of my scripts and it works, however all of them were real life sources, so I have no idea how good/badly is gonna behave with anime. I guess we're about to find out.