I think you are being impatient and should give it more time.
BUT, depo is notorious for causing weight gain and hard weight loss. My 20 year old sister, who is about 105 pnds and has the metabolism of a hummingbird, gained about 10 pounds of FAT while on depo. She decided to stop and has since lost weight.

Also, depo wouldn't cause low carb to be ineffective; the type of diet wouldn't matter.