I need some help reproducing this issue. When I drag and drop a gcode file for the first time, it works. Once I finish a job, drag and drop another gcode file. Click run in the gcode widget. It is still running the old gcode file.
My machine is running a multi-hour job at the moment. ;(
I’m having this issue as well, and today when i went to test a modification to my Z, i couldn’t even send geode, it just runs through the list and says sending complete.
Perhaps you had an issue with the recent jsfiddle timing out. The issue has been fixed. Can you try reloading with force_reload=true once?
I just tried running a job, and then dragging/dropping and it works fine. Here’s my theory. The browser limits localstorage() to 5MB per domain, i.e. for http://chilipeppr.com. How big are your Gcode files?
Only 784 lines. I will try to reproduce the issue on another workspace. Perhaps I broke something on my workspace.
Does the Gcode widget show the old gcode? or the new gcode? Or does it only run the old gcode behind-the-scenes, but show the new gcode in the Gcode Widget? If you scroll up/down from start to end of Gcode, what code shows? All of that widget looks at an array called this.fileLines[]. Is it possible that the array is not getting reset on your new file?
@Jeremy_Bartos Are you running the latest Serial Port JSON Server 1.7? The Gcode widget now sends via the /jsonSend command and that’s only available on the new SPJS.
@jlauer I believe the gcode widget shows new code. The 3d widget has its view updated to the new code. Click the run button and the old code is executed. I might need to double check that the gcode widget show the old code. Many of my codes are very similar. 
I updated the JSON Server to 1.7 and that fixed the issues with the Gcode and Viewer. i’ll test it more tomorrow, but it looks like it’s been fixed. I’ll be trying a test cut and i’ll reply with any updates.