I suspect there might be something interesting going on with your helm-mode activiation/config. At any rate, helm-find-files, as well as helm-M-x, were removed from default-on status in helm-mode by this commit.
I wonder if you can get that functionality back by customizing 'helm-completing-read-handlers-alist'. In that structure, one option is to delete:
Alternatively, you can also set those entries to:
There is a third option, but it will be left as an exercise for the reader.
For what it is worth, when I first started using helm, helm-find-files especially caused me some serious confusion for a bit, in that a back arrow dropped a whole word instead of moving characters around. I am not responsible for this change, but I think it makes sense. As for your issue, I think maybe the alist is somehow getting processed by default but not for new instances or something?