RE: N jobs 1020 takes a day to complete downloading
I am then not sure why you are talking about N Jobs in context of R3 - as I remember those types of jobs existed in R2 only and R3 has just Jobs (without N or A). So, as I asked earlier would be good to know what exactly build CU you are using.
Also, please tell me how exactly you validated that the delta is not sent, please note that first time you execute a job it will send all the data (just because it is FIRST time and nothing was sent yet) but if you execute the job second, 3rd, ... time it will send delta only. So, I would like to see how exactly you validated that the delta was not sent for not Initial (first time) sync.
Please also note that CDX uses SQL Change Tracking to be able to send the delta, the SQL Feature itself has Retention Period set to a number of days, what it means for you:
if let's say that period is 2 days but you execute the job every 3 days then you will never have delta - you will always experience Full Sync - please check that setting in your SQL Server Management Studio and then "map" it to a frequency your jobs run with, probably this will explain why you are experiencing Full Sync instead of Delta Sync.