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Yeah something is being flaky - I'm not sure but it sounds like you could be hitting a resource limit on the server? Are there any limits on your server put in place by your hosting provider? The fact that it originally stuck at:
"validating filesystem is prepared for updates"
Is the step where the marketplace module checks the modules/skins directory and ensures it has write permission before starting. It sounds like it could be bombing there.
I see you're running PHP via PHP-FPM - make sure you have enough worker processes so it doesn't hang.