I think this is the "refresh" issue that Service Desk has had forever. The one thing you can do is open the form up in a new window rather than a javascript pop up. You can do this by going to Admin -> Service Catalog -> ServiceDesk (or whereever your forms are located) and there will be a orange lightning bolt beside Submit Ticket to Service Desk (Advanced).
Click on it -> Edit Form -> Check Open In New Window and click Save. When Service Desk refreshes it won't affect the form because it's open up in a new window and not a javascript one. You can tell because it won't have the gray border and has the IE one.