Hi,
What version of 2d toolkit are you using? I have not had any similar issues with latest on 2.5.8 in both Unity 5.6 and 2017.1.
"Importing small assets" only comes up once per project for the most part. Unrelated to 2D Toolkit though, this "importing small assets" thing seems to happen much more frequently in all my projects (including those that don't use 2D Toolkit, eg. 3d projects) so I don't think its related. I have seen new (virtually empty) projects do this on each save
Re: the freeze, if you are on the latest version, and are still having the issue, submit a repro if possible to private support and I'll investigate.