I analyzed 2 nearly identical flying wing in XFLR5, how come the one with the thinner tip chord has a higher cD?
It may be inaccuracies in your modeling method; it's hard to say without more info. 

First, this isn't quite an apples-to-apples comparison. The aspect ratio of the first wing is higher than the second wing, so you're varying more parameters than just the tip chord. 

The way to think about this is that the CD of a wing is going to be strongly dependent on the aspect ratio $AR$, the taper ratio $\lambda_T$, the chord and twist distribution along the wing, as well as the airfoil distribution. Is the airfoil t/c constant across both wings? That will also have an effect.

It would be clearer to look at a polar of CL plotted against CD; the best point of comparison is to look at the drag generated at the same CL, not the same angle of attack (because the zero-lift angle of attack will change with wing design as well). The second wing is generating less drag, but also less lift at a given angle of attack; the comparison isn't really fair. If you're using a VLM what you're measuring is the CDi of a wing geometry, which is going to be most strongly dependent on CL.