I've recently run across someone else who also asked about a cloud based storage issue. I asked them to open up a windows command prompt, cwd to the directory, and try to list the contents with dir. For whatever reason that didn't work for them, so could you see if that works for you? I have no idea why explorer would be able to see files that lower level tools like dir can't but it appears that is what was happening. Permission issues might be involved. Make sure you're running ioftpd as the same user the files are being accessed as when testing. Double check that directories aren't marked as system or hidden.
Assuming you can see the dirs/files, the next thing to try is turning off some ioftpd features. Try setting 'NTFS_Reparse_Method = IGNORE'. This turns off the fancy logic to cache NTFS links/symlinks as links and not the target dir, but it might be getting confused with the cloud stuff.
The other thing to look for is entries in the error log. ioFTPD should warn about any mountpoints in the .vfs file that can't be accessed. It only does this the first time the .vfs file is accessed, or after any changes, to keep log spam down but you should see the error code it's returning. Let me know what is says.
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