Jessali, the problem is with the PHP.ini settings.
BackWPUp sends a crap ton of POST variables and, unless your .ini file is setup to handle that many, it will drop some of the variables
We had to set ours to 6000 from 1000
; How many GET/POST/COOKIE input variables may be accepted
max_input_vars = 6000
Same exact problem as jesseall
+1 same problem as everyone else. Trying to add a job for s3, but saving the job losses the settings.