Are you using menu File>Save or menu File>Save As?
I can save/save as, and it asks me if I want to replace it. It's as if it's spontaneously creating a duplicate document that has no home on the hard drive.
If you use save and there is a backing file that can store the documents content you should not get any prompt the file should just be saved updating the backing file.
If you opened a jpeg and add some layers an use save without first flatting the document Save will switch to Save as and may default to "save as" to type PSD and filename JpegName.PSD. If there is a file with that name existing in the output folder when you click save you will be asked if you want to replace the existing file. You will get the prompt when ever you use save as and the output file already exist. If you make the nane unique and click save you will not get that prompt.
If the output file is being created before you use "Save AS" it would not be something the Photoshop would do spontaneously something would need to have been used to do that an Action, script, Script event handler, plug-in. Photoshop does not spontaneously create file. Photoshop does have bugs but I have not seen one reported about Photoshop creating file one it own.
I know I shouldn't do that, but that's what it's doing.
Here's one example of how I can reproduce it:
Option double-click on a PSD in InDesign.
The PSD opens up.
I 'save-as' the PSD in another location.
Make a couple of quick edits (add a layer, for example).
If I click the document's icon in the tile bar to drag the edited image into InDesign, the icon vanishes, and the title bar becomes useless. You can't command-click on the title bar to locate it in the finder, either.
However, if I make another edit, the icon appears again, although grayed out, since it is an unsaved edit.
Hit 'save' again, and the icon returns to full color, but once again, vanishes if I touch it.
After this, my only other option is to go back to InDesign and navigate through the folders to place it. Or, drag the PSD from the finder to the InDesign doc.
It's a shortcut I use quite a bit, and it's suddenly stopped working.
I can not reproduce your problem for I do not install or use other Adobe applications I just use Photoshop. I have no knowledges of how Adobe products intergrate with each other. Perhaps InDesign is creating your problem. You also wrote that you double click on the PSD file in InDesign therefore the file exists. If the file exists and you use Save As in Photoshop and try to save and existing file you will be prompted with that do you want to replace the file. Normal operation. You should use Save not Save As if you opened the PSD document in Photoshop and are working on it..
Yeah. I figured it's probably a glitch on my end since I couldn't find anything on Google. Thanks for looking into it. I appreciate it. I'll reinstall InDesign. If that doesn't work, I'll do the whole-she-bang with the hard disc. In years past I could work around these sorts of things, but this is driving me crazy.
I figured this out after reinstalling OS X, downgrading to Photoshop 7 and experiencing the same issue. It's a freaking Suitcase Fusion plugin. Disable it and the problem goes away. Unbelievable.