seeing this in both our production and test environments with 9.96. It's super annoying. When you drag packages into configurations there is a delay and sometimes the packages to actually go. Running 10.11.6
Bump. Still happening for me in 10.12.3. Sometimes I drag a package to highlighted config X and it shows up in config Y anyway. It's more than a nuisance at this point if packages are going to the wrong config, even when I'm trying to be careful.