Tupac said in an interview that there was a point that he was just going in and laying down verses for cash, since he was broke due to all the legal troubles (talking about the time he got shot). He was probably paid for the work he did with puffy and biggie, so they would most likely have the rights to it. Runnin' was meant for Thug Life, so Biggie was probably paid for his verse there by Tupac's peoples, so that's why Amaru retains the rights for that.