It was only the opinion of the OP that thought running WR had messed things up - the helper did not corroborate that and as the OP did eventually get updates, I don't think WR had anything to do with this problem and it was a problem on MS's end.
Many who haven't even heard of WR have been experiencing the same problem - that is why MS have been releasing monthly updates to ease high CPU and memory usage when in a manual check for updates.
Where the natural update methods have caused problems, WSUS Offline Update has prevailed.