Was the backup in progress while you were having this problem?
I was opened up an old project (probably from Sonar 8.5 or X1 and it was taking forever to load, when I noticed my weekly backup was running!
If no settings/hardware/software changes were made it sounds like something might be running in the background.
Are you using a laptop? Your external HDD is powered by the USB? That might be a drain, see if there is an ac adapter that can power it.
I was using a laptop ages ago with my M-Audio Fastrack Pro powered through the usb. Real trouble, as soon as I got some dedicated power for the Fastrack it was working fine.