This KB article may help:
http://kb.juniper.net/InfoCenter/index?page=content&id=KB16326&actp=RSS
From reading it I get the impression that if you boot from the internal flash, then you can't snapshot to the internal flash, I'm not sure if there is any way around it, a bit from the KB article:
The purpose of the snapshot is to save a copy of the current Junos software and configuration on an alternate device. If the device is booted from the internal flash , then snapshot will backup the internal flash to a specified alternate media (e.g. USB) .If booted from external device then snapshot will backup to internal flash.
Example of the device that was booted through internal flash attempts to snapshot to same internal flash will throw the below error:
root> request system snapshot media internal re0 slice alternate
re0:
--------------------------------------------------------------------------
error: cannot snapshot to current boot device