Maybe I didn’t articulate the problem well.
I’m hosted on Rackspace Cloud Sites and it’s a bit quirky. Instead of waiting an appropriate amount of time for a website to finish processing it will give an “no available nodes” error. I actually figured out that I can cause it to continue and the process will finish.
I’ve just now realized that when I updated Plugins, that the ARQ seems to be updating the Backups in the various folders. For this site in question, the number of files being backed up in wp-content was 1741, which prompted a note from your plugin that the number of files seemed excessively large. Once I would update a plugin, I would click the link that your plugin generates to click if I’m updating a plugin or theme. I believe your plugin is then updating the backup files. When this was happening it took longer than the Rackspace Cloud Sites and was timing out with the error. In the past, I was just skipping over this because of that error and I think it was messing up ARQ for that site. I guess I don’t know what the consequence is if the ARQ does not get a chance to update the backups.
Instead of excluding the entire themes folder, I’ve excluded the images folder of the primary theme. That folder had 1300 images in it so the number of files being backed up in wp-content is now less than 600. After updating plugins and clicking on the link for your plugin, the process completes and states that everything is updated.