Try doing a "quick format" of the SD card and then copy the update over to it again. That's what I had to do the first time I did a SW update. I had the same issue as you. Now I always format the card first before doing an update.
08 Skeeter SL210, F225 Yamaha four stroke, 798CI SI NVB, 997C SI
(formerly owned an 1197C SI NVB Combo)