Thanks guys for getting back to me. I re-downgraded proftpd-mod-vroot to v0.9.2-2+b2, deleted all shares, restarted the service, upgraded to 0.9.2-3, created shares again - then the shared folder was not empty anymore.
At the end, I only had to reset ACLs for consistency, and played a little with folders/files privileges. So it looks like the above workaround is working, probably it was a layer 8 issue on my first attempt
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