Is is better to backup all partitions in one backup or do each partition in a separate backup?

Is is better to backup all partitions in one backup or do each partition in a separate backup?

We have some partitions with over 500K files on them.

I bring up this question because this morning I was unable to restore files from a directory that had 40,000 file in it and it's sub directories. B&R hung when trying to display the files in the backup. After an hour I killed the MMC. I got tired of waiting and windows said B&R was unresponsive. I tried several times to do this operation. I even rebooted the server but it didn't do any good.

I'm using B&R 10.

From what I've read in other posts I don't think I want to go to version11.

And actually I got started using Acronis products with True Image Home and the Disk Director Suite and I never had the problems with them that I've had with the comparable server and workstation products.