We are also seeing this problem. I have multiple folders that i've deleted multiple times, but they keep coming back! We have about a dozen machines syncing, a mix of PC's, Macs and one Linux box. They have versions are on the latest 2.3.3 About half are usually online, but some are offline for long periods of time. The share is rather large, about 27 GB.
I can supply debug logs if it will help.
I've been noticing this problem off and on for over a year. IMO, this is a critical issue and one that needs MUCH more attention.