Well you've been told the workaround, ranting at people for trying to help wont get you anywhere. Maybe Dish will read this thread, maybe not. I highly doubt that anything will be done about this anytime soon. You are far from the first person to complain about this flaw. Hopper has been out for a year now and they haven't bothered to fix this. Like it or lump it. They'll fix it if/when they want to.
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I don't think it's much of a flaw but more or less that the internal drive in the receiver can be read at a faster speed then the external drive. It takes my Hopper 70 minutes to do the nightly SIC scan. I think roughly 10-15 minutes of this is the internal drive (the less disk space used the faster the scan) and the rest is my USB 2.0 External Drive (60-55min and once again scan varies on how much data is on your drive)
I do agree it's annoying. Especially when you get home late at night and decide you want to watch a TV show or movie but you want a snack first. You queue up your DVR program, walk in the kitchen and grab some popcorn or sandwich and come back and your Hopper is 5 minutes into the scan.
The ways around the long scan
1) Schedule a junk SD recording at 1am-2:30am
2) Remember to disconnect your EHD or just get into the Habit of plugging in your EHD only when you want to use it.