Alright, logging it to a file then. Is there anything in particular I should be looking for?
Edit:
logged the sync debug, all of the rows based on my random skimming are
2020/05/05 12:58:08 DEBUG : Photos/iPhone 5/2013-09-19 06.48.40.png: Unchanged skipping
2020/05/05 12:58:08 DEBUG : Photos/iPhone 5/2013-09-19 06.53.46.png: Size and modification time the same (differ by 0s, within tolerance 1ms)
So no actual issues. Even the .DS_Store files are synced. Maybe something is different in terms of accounting space taken? But that still doesn't explain different files count (maybe folders are not counted in rclone/b2 and counted on Ubuntu?)
Generally, I check for ERROR first and it depends on what files aren't synced. I would try to isolate a file that did not work and check for that in the log and see why.
Usually counts are off because rclone doesn't have access to see something which isn't always in the logs.
Each one is a bit unique so it's a matter of looking through the log and going from there.
What you want is rclone check which will check the source vs the destination and tell you exactly what is missing and what isn't.
Also try using rclone size on the source so rclone size /path/to/files then at least you are using the same tool on both so we don't have to worry about GiB vs GB etc.