In layman terms, the order of execution might not be correct.
In some circumstances, totally isolating the system can cause it to sound sterile. However, I am not sure this is the case since the rack/component interaction hasn't been properly described. Although, you do seem to try to kill vibration with your application of sand and mdf boards. I think this is more relevant than the rack/floor interaction.
Also, generally, in applying draining and deadening techniques to system, one wants to drain vibration from component to something that is "dead". You seem to have this backwards. And, this seem to lessen the effect your rack/floor interaction has on your system's sound.
Lastly, as the rubber cup is under the rack now, vibration is not drained as expediently as when the rack's spikes are directly touching the bare floor. This ought to slow down the velocity of vibration traveling in your rack if there is any significant vibration still moving around. I don't think this is very relevant since you got the sand and mdf applied to your rack.
In some circumstances, totally isolating the system can cause it to sound sterile. However, I am not sure this is the case since the rack/component interaction hasn't been properly described. Although, you do seem to try to kill vibration with your application of sand and mdf boards. I think this is more relevant than the rack/floor interaction.
Also, generally, in applying draining and deadening techniques to system, one wants to drain vibration from component to something that is "dead". You seem to have this backwards. And, this seem to lessen the effect your rack/floor interaction has on your system's sound.
Lastly, as the rubber cup is under the rack now, vibration is not drained as expediently as when the rack's spikes are directly touching the bare floor. This ought to slow down the velocity of vibration traveling in your rack if there is any significant vibration still moving around. I don't think this is very relevant since you got the sand and mdf applied to your rack.