It's briefly loading your settings for that document when you switch, so it is normal.
Just to add a bit of context to this: Aseprite scripts/extensions all run on the same thread as the rest of Aseprite and thereby also the UI. So anything the script is doing will be blocking for the UI, ie. if it takes a bit of time, the UI will be frozen while it carries out. When you switch tabs, I need GM Link to adjust to the project info that has been configured for that file, and it does so by reading from the config file on disk which is usually really fast but can still be felt briefly. I'm not saying it's impossible to do something about it, I just haven't been looking long enough for it. I will try to implement it if I figure something out at some point. :-)