2011s have different file structure. and it has NAND flash.
you have the flash there accessible as "/file"
in the more recent platforms with usually less flash in there, /file points to a ram-disk, and the actual flash
contents are accessible in the sub-directory called flash. everything else will disappear on reboot.
early CRSes had also quite large (128MB) NAND flash.
CRS112 has SPI flash (as almost everything since hAP lite), and is significantly smaller now. (16MB)
discussion about this:
http://forum.mikrotik.com/viewtopic.php?f=3&t=106195
you can also check it out on routerboard.com, some boxes have storage listed as NAND, the newer stuff
has it shown as FLASH.
anyway, the issue you described is strange, it shouldn't be so.