When you start MATLAB, it first looks for a preferences directory that corresponds to your current release (in this case R2025a). If it cannot find a preferences directory for the current release, it will automatically look for an old MATLAB preferences directory and automatically import your settings and history from that old preferences directory. Your best bet, when upgrading MATLAB, is to not manually copy any files into the preference directory. Your best bet is to let MATLAB handle that for you.
Upgrading from R2024b to R2025a should be able to convert your R2024b preferences into the new R2025a format and that should happen automatically. This process should work when upgrading from R2024b to R2025a, but the format in which preferences are stored has changed, so you could be encountering an edge case.
I'm curious if you used the beta of the new desktop? I know some of the settings import/conversion process wasn't working perfectly in early beta releases, so I wonder if the issue you are encountering is because it is finding incomplete preference information from the R2024b beta. For example, MATLAB R2025a starts, it doesn't see an R2025a preference folder, so it looks for R2024b. In the R2024b preference directory it finds two sets of preferences: (1) the old desktop preferences and (2) the preferences from the beta that were not imported correctly. Because it sees preferences in the new format, it is using those instead of the preferences from the old desktop. This is just a theory.
Here is an experiment you can try:
- Rename your R2024b and R2025a preferences directories to something different (effectively: give them a name so that MATLAB doesn't find them, but don't delete them so you maintain a backup).
- Create a new empty preference directory with the name R2024b (not R2025a).
- Copy XML files that have your preferences from your backed up R2024b preference directory into the new and empty R2024b preferences directory (instead of the R2025a directory).
- Now start MATLAB R2025a.
In theory, this should detect that you don't have an R2025a preferences directory, look for an R2024b preferences directory, and find just the XML files, which it should then import into the new R2025a format.