Hi Patrick
Thank you for your comments. I actually use PCA to reduce dim of my latent space and  then plot that.
After training my model, I can see that reconstruction become awful   Actually trained model can not even reconstruct the input roughly.
I would guess that sth should be wrong in my codes. I tried many things however, could not find that. May I ask you to take a quick look to my model and see if you can find my mistake?
zdim = 20
Beta = 3
ps: classic AE gives me perfect result however this one almost gives me nothing.
I appreciate you time,
Wash your hands after reading this massage, 
Pedram