I can't reproduce it with a directory ending with .com. The first poster does not use a directory with .com.
Can you post a screenshot of SmartFTP showing the folder tree/list when it is not working and one screenshot when it's working?
Behavior was that the directory with the ".com" name would not update and display contents. Empty explorer box (no files, no folders, refresh did nothing, no squawks about existing files if you dragged one over). Oddly enough, the sup-folders appeared in the directory tree. And files would display normally in the other sub-directories.
This behavior was exhibited while the 2.0 client key existed in the registry. That may be the root cause. I've since deleted the old key and things have cleared-up.
Sorry, didn't take any screen shots at the time as my focus was beating it into shape to get work done, not debugging the tool.