Jacob Sullum's theory:
It's plausible that Obama, embarrassed by the proliferation of medical marijuana dispensaries on his watch, worried about Republican accusations that he is "soft on drugs," a charge perenially hurled at Democrats, even when there is very little evidence to back it up. Given his comparatively candid discussion of his own drug use in his memoir Dreams From My Father, Obama might have thought himself especially vulnerable to such criticism. Hence he let the drug warriors in the Justice Department do what drug warriors do.
The other option is that the abuse of medical marijuana laws in, say, California and Colorado, has weakened his hand vis-a-vis the DEA. Both states have effectively legalized the drug for recreational use, with a fig-leaf over their juicy, sticky buds. I'm with Sullum and wish the DEA would back off. But I also wish some states had exercized more discretion and care in allowing for medical marijuana.