We were at BLT 2/24-3/2 and never could make online check-in work (using Firefox)...contacted MS and they told me they were having problems. Gave me a "work-around" using My Disney Experience, which I decided not to try...just don't want the headaches of yet another Disney IT set-up that not only might not work, but might mess up what does work!
Anyway, we got to BLT and had no issues checking in...the CMs behind the front desk were painfully slow (took almost 40 minutes to check us in--two different CMs (and my daughter's was slower than mine!) and we were making no changes and had no particular issues...the CM whose station I went to wanted to do both of us, but I said no, that they were separate reservations so my DD could go to a different station...good thing; we might still be there if that same CM had done both of our check-in's!
Anyway, no one did anything "wrong"...they were just incredibly unbelievably slow!
Not sure online check-in would have appreciably hurried the process, tho...as the CM grabbed an already prepared packet (including a room key) when he finished doing whatever it was he was doing on the computer for so long...