theres a file that keeps reflashing stock recovery.. search the forums on what it is, i forget. its something called install-recovery.sh or so i believe
edit: navigate to /system/etc/install-recovery.sh and rename to something else or delete it..... then reflash recovery, and it should stick
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Nexus 5 (D820)
: Purity | Franco Kernel
Nexus 4 (E960)
: Carbon | Franco r193
Older devices: Galaxy Nexus, ASUS TF101, Nexus S, Samsung Vibrant, G1