There is another possibility that come to mind that deals with caching issues. nxTools copies the directory over to the target including the .ioFTPD* files which contains the permission info, then changes the ownership. In my mind it should do that in the opposite order, but no biggie. Given that order, the first potential problem deals with a known bug in the way the directory entry for a subdir isn't properly invalidated in the parent. This usually shows up in the common problem of the directory info (size, perms, etc) being wrong when viewed from the parent which is how users almost always view directories. The way to see if this is the problem by viewing the raw directory instead. In FlashFXP goto directory->View Raw Directory while in the directory and look at the first line for the "." entry (current directory). This is the actual permissions, owner, etc used by ioFTPD internally. Is this correct? If not, issue 'site refresh' and re-list to force a cache update for the directory and see if it changes. If it does then we might have a new problem I'm not aware of or the bug is actually in nxTools.
I'm assuming that all worked correctly, BUT you normally only see owner, timestamp, etc when viewing the directory as a subdir and that DOES have a known bug (not sure when it got introduced) which is already fixed in the next release of ioFTPD. The simplest way to test this is from the parent so just issue 'site refresh' and re-list and see if you pick up the correct info...
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