do you mean while the content is being transfered? or once it's loaded in the HD?

if it's during the transfert, my tone is also affected and sounds different from the one I get when it's over for some reasons

..not clean but not as tight/full I'd say

I have the same issue, and when it happened to me tonight I know for sure the amp was enabled, all the settings were saved and brought back when I dialed in the patch... But the distortion just wasn't there, I got a clean tone. The amp was the treadplate and there were no other effects, and the drive was up, the amp was enabled, etc etc. It was only when I switched off the patch and to a different bank, then came back to it that the distortion in the amp model was there.

In other words, I can no longer count on the amp model affecting the guitar's sound every time I call up the patch. Very scary indeed.