RC timer not reaching desired voltage
To get the BJT to work properly you need enough current to flow through the base terminal, and in your case due to the high resistance you are only getting: 
$$ I= V/R $$
$$ I = 1.2/10^6 = 1.2 \mu A$$

Thus the base current is too low to function. While when you reduce the resistance to 1K ohms only, the base current will be 1.2mA which is sufficient enough.