Recently I updated to the latest GimpPortable using the auto install method through PAM. This is not the problem, it worked flawlessly and all of my settings were retained 
The question I have however, is if this method is recommended for all applications, particularly gimp because...
I ran into a small problem the other night trying to edit some photos I took in Greece. They're 7 megapixel, and from a 3meg jpeg inflate to about 40 megs a layer. I duplicated the background layer 3 times to apply some affects and adding another blank layer would cause gimp to lock up for minutes at a time.
This was never an issue before with the previous Gimp that was packaged with the software suite. So I had a go with that Gimp doing the exact same procedures with the same picture and experienced no problems. I tried the same thing again in the problematic Gimp (upgrade install), and it locked itself up once again.
For my next attempt, I did a clean install of GimpPortable instead of just upgrading the existing version like I had done prior. Everything worked as expected this time, no lock ups!
If you experience any problems, you too may want to try a clean install if you've recently upgraded.
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through the menu (the so called "in-place-update") should work with all apps. It is an important feature/part of the PortableApps.com collection.
“Science is the belief in the ignorance of the experts” - Richard P. Feynman
"What about Love?" - "Overrated. Biochemically no different than eating large quantities of chocolate." - Al Pacino in The Devils Advocate
GIMP Portable 2.2.15 can install right over 2.2.13. It will overwrite all existing files and there's nothing in 2.2.13 that's not in 2.2.15... so it's not like any old files are left behind. Is it possible you added something (a plugin, etc) or changed your configuration in 2.2.13 in some way that would affect 2.2.15?
Installing 2.2.13 and then installing 2.2.15 over it yields an install identical to a clean 2.2.15 install. I just double-checked it.
Sometimes, the impossible can become possible, if you're awesome!
So doing a clean install of 2.2.13 and then another install of 2.2.15 when no configs have been affected by launching 2.2.13 before upgrading sounds like it should work just fine, and did according to your tests.
Is it possible that any settings created in 2.2.13 (from usage) are retained and therefore affecting the 2.2.15 upgrade? I used 2.2.13 quite a bit during my gimp learning process, however I am not using any plugins or scripts.
Less is more
2.2.13 with 2.2.15 over it and a 2.2.15 are binary identical... as I said.
Your settings are, of course, retained. Don't know what config you could have changed that would have messed it up.
Sometimes, the impossible can become possible, if you're awesome!
that the way the user data is stored (=some files in the /Data folder) changed from 2.2.13 to 2.2.15?
“Science is the belief in the ignorance of the experts” - Richard P. Feynman
"What about Love?" - "Overrated. Biochemically no different than eating large quantities of chocolate." - Al Pacino in The Devils Advocate
In which case GIMP should update any changed files... as it would on a local install.
Sometimes, the impossible can become possible, if you're awesome!