I notice lately my backup files have been the exact same size 3.99 GB. My site has been steadily growing however so this didn't make sense. I went ahead and opened one of the backups and it said Unexpected End of File?

Ah, maybe cPanel is limiting the size of the backed up data.

Is there any way around this? I'd hate to have to copy paste the entire site directory...

Well, you are doing the following, right?

cPanel > Backups > Generate an Entire Home Directory Backup

Right? Or how else are you doing it? Remote FTP?

I am generating a full backup yes.

maybe the problem is you have only 3.99gb of free disk quota

Don't quite understand. Could you elaborate? I thought being admin meant my quota was unlimited...