Set your sort order to By Capture Time or By File Name
Once you are done with all of this editing, then you can set the custom sort order if you want.
There is a setting for that. It is in the Export dialog window but whatever you chose will be globally applied. You have to first select an image, click Export, in the Export to area select Same folder as original photo, check Add to This Catalog then Add to Stack and then select either Below original or Above Original.
It can also be changed for individual stacks by Right Clicking on the stacked image then hover over the Stacking entry and another list pops up where you can move up or down that image in the stack.
I personally want all stacked images to be below the original. I don't want a stacked JPG, PSD or TIF to be above the original RAW files it was created from.
You have to actually Export that image to have the settings take hold. If you click Cancel all those changes you made will be forgotten.
Another Also is if you are sending an image to PS or some other external editor check "Stack With Original" in the external editor tab of the preferences.
Thanks for your reply ... this is the most common answer I come across, but it does not address my issue. My problem is I am working with 1000s of files from multiple photographers and even though we are time synced, I still want to be able to reorganize the images in a more cohesive fashion as I see it while I edit them ... for example, I would like certain sequences of the bride getting ready to be in order and and not interspersed with the photos the other photographer takes of the groom during the same timeframe and likewise ... I generally sort by capture time and then adjust manually as I move through the take. I want to use the custom order option, but am dismayed that any images exported to Photoshop and then saved are then moved to the back of the film strip. This, to me, defeats the entire purpose of a custom order.
I understand that isn't the answer that you are looking for. But I have found that sorting the images by filename is the best way to keep the images together and in place. I find that Lightroom on my computer always seems to change the sort order to capture time after I import new images. And I find the behavior the same as you are seeing. I'm using Lightroom CC 2015.
I had the same problem. I think I figured it out, depending on how your photos are set to be arranged.
For whatever reason, all photos in my stack (one photo, and the edited photo from PS) were moved to the end of my sort. I had to select the EDITED image in the stack and move it to the end of the stack (by moving it down in the stack). This way, I think, the images would sort according to the image at the top of the stack (the original image with original file name needs to be at the top of the stack), and then all of them would magically get back into its original order.
I hope this solves your problem, like it solved mine!