I have a similar problem with the Presonus Audiobox 1818. With Ubuntu 12.10 I had the issue appear often, but turning the card off and on (often a few times) would eventually fix it. With Ubuntu 13.04 I found no way of doing this. I installed Ubuntu 12.04.2 and it seems to work well all the time. I don't know exactly what the problem is with later versions.
Other things which may be affecting the behaviour of your card:
- In Ivy Bridge machines, try using a USB 2.0 port, if available, instead of a USB 3.0 port. Your computer may have an option in the BIOS to switch the ports to USB 2.0 compatibility mode, which should do the trick too.
- There are reports of Wi-Fi cards and other USB devices causing crackling in USB audio devices, so you may want to disable them temporarily to diagnose the problem.
- There are reports that disabling Pulseaudio may work around crackling problems with USB audio.
- Some bits of the set-up for real-time sound recording may be applicable here.
As for the driver stuff you mention in the comments: the Audiobox is a class-compliant USB audio device, which the Linux kernel supports without the need for any third-party drivers. Bear in mind that there are several reports of crackling problems with USB soundcards in the Presonus forums, even with Windows and OS X, so this issue is likely to be hardware-related in some obscure way.