@Purity it's probably the shared hosting thing.
There is a really huge amount of work that updater needs to perform, and it takes considerate amount of server's resources to do so. Updater tries to be smart about it, and splits the work into series of small work items / chunks. The size of work item is determined by the Server performance settings option:
But in the end, your server is expected to complete every chunk atomically - in one request. That means, for example, that your server must be powerful enough to to add 400 files to the backup zip file within once request.
Shared hostings can employ multiple measures to ensure that one site will not consume all the server's resource. It can calculate how much CPU/Disk IO your site used within the last few minutes, and it can start throttling resource allocation to your site if you exceeded some limit. That can include decreasing of max-execution time, lower priority for IO operation, lower priority for PHP process, etc...
This resource throttling is only fair --- your hosting provider have to ensure that other sites hosted on the same server won't be affected by your actions. But it can mean that long-running tasks like updates / data import / export / image regeneration / cache indexing / ... can fail.
This is definitely a red flag, and you should consider different hosting solution.