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This is happening in two sites I've restored using BackupBuddy*. One is single, the other Multisite.

.* this may render the question as "too localized", but maybe it could happen with any other backup/restore tool

Whenever upgrading (single or bulk), the message appears: "The update process is starting", the spin keeps spinning, but doesn't goes past this point.
If bulk upgrading, only the first upgrade is shown as in progress.

I give it a few minutes to be sure. All updates were successful and the site is not in maintenance mode.
WP_DEBUG doesn't report nothing. The server error_log don't have any info. The browser console don't throw any errors.

I tried to delete the update_plugins transients, but now the update gets stuck in the message: "Downloading update from..."
It completes anyway.

Looks like all of this is handled inside the file /wp-admin/includes/class-wp-upgrader.php, but I can't find any hint inside of it.

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    I have the same with the Pronamic plugin (ocassionally). It is a plugin with 1600+ small files. Haven't seen issues yet (maybe everything updates and it's just the confirmation message missing), but I know I'm not using all 1600+ files ;-)
    – Jan Doggen
    Commented Sep 15, 2015 at 18:04

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Don't know, but maybe the issue could be in file permissions? There could appear files with other owner or blocking permissions after restoring and it blocks upgrading process.

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    You raised the very point I was missing in my debug process: file permissions. I deleted all WP files (except wp-content and wp-config, of course) and replaced with fresh ones. Bingo! Thanks, Eugene.
    – brasofilo
    Commented May 16, 2012 at 11:40

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