If you put the save cover part in the proper place, it will only save a cover if it can't find the ASIN number. Is it for one that can be found. If it has a valid ASIN number, your Android/iOS device should download it automatically.
Edit:
I just thought of this. I did change the script a little. The modified line that you should put in is this.
Code:
C:\Users\m0ngr31\desktop\kindle\mobi2mobi.exe --savecover "cover_!asin1!!asin3!!temp1!.png" "!filename!">null 2>&1
Let me know if that works

I've edited the post above to reflect the changes.