Make sure the remote is un-linked, then pop the batteries out. Unplug the hopper. Put the batteries back in (or better yet replace them) and see if it still keeps doing the all blinking thing every time. It may blink back and forth the first time you press something, so try again.
Make sure that remote has not accidentally linked to any joeys if you have any (just try power since there won't be any service). If so, unlink from those.
Plug hopper back in. Check that the antenna is connected on the back. Press system info button on front panel and then press Sat button to link remote. Try a few times, if it won't link the remote is probably bad. Only thing I've seen for that issue.