If one of your apps causes what is called a kernel panic, the device will reboot and ignore the SD and boot directly what is installed on emmc. This was an issue with the early builds of CM10.1 running from SD and has been corrected in later builds. But it may still happen occasionally.

Sent from my BN NookHD+ using XDA Premium HD app
See my Nook Color Tips Thread here,
and my Nook Color EMMC Partition Repair Thread here,
and my Nook Color Updated CM SD Installation Instructions here,
and my Nook HD/HD+ stock tips thread here
and my Nook HD/HD+ CWM Root Tools thread here
e.mote's Nook HD/HD+ Dummies Guide for installing CM10.1/CM10.2/CM11 here