I have this same problem and I have done both things you said above.
I've spent more time on my iPhone safari lately and recently did a reorganization of some bookmark folders because we are shopping for a car and I had a lot of tabs open on my phone that I wanted to open on my MacBook pro. Instead of tediously using airdrop for every single tab my iPhone had open, i simply made a bookmark folder and placed them all in there. I thought I would be able to open bookmarks on my mac and easily click each link in that folder to open them. Nope. The bookmarks on my MacBook do not match my iPhone and nothing new is reflected there. The folder I created is not there either.
I toggled iCloud safari syncing on both my MacBook and my iPhone and it is still not showing my iPhone bookmarks. I have everything turned on properly and tried rebooting both devices too. Nothing is allowing me to force sync all bookmarks on my iPhone to the cloud.