USB access hangs causing CPU load to increase

I have a CC9U reading data from an ADC and writing that data to a USB stick. I’m also ftp’ing the data via ethernet. It all works fine at low sample rates, but at higher sample rates, it runs fine for a few hours, then the CPU load suddenly increases exponentially. When this occurs, the usb-storage process is in the D state (uninterruptable). The only way out is to reboot.

Any ideas?