I have this problem since Webstorm 10 and I can't seem to find the cause of it. Every time I want to create a new file using a template it reformats it. Problem is that I don't want that. Of course the IDE has an option for that but whenever I close the IDE and open it again, the checkbox is marked again. I tried invalidating the Cache and all but it keeps happening. I hoped Webstorm 11 would fix this, since I create an ticket on the Issue Tracker but I start to think it has something to do with my setting, I just can't figure it out. Maybe somehere here had the same problem and has some insighte for me.
Here is the link to the issue on the tracker: https://youtrack.jetbrains.com/issue/IDEA-141467