Theres a few other things you can check

• Try checking the allowable file extensions on the host/host settings page, add your file type if its missing (AFAIR swf is there but its good to check)
• try it a few times (make sure your doing so via host->file manager) and try a ctrl+F5 to force a page refresh
• If you created the folder in File Manager as a "Secure - Database" folder it would NOT show up via FTP so check the type of folder..
• finally check your event viewer to see if there any issues logged.

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I missed this an error on the log, but it does not seem to coincide with my trying to upload the file or synchronize. Nonetheless the error looks ugly, but has no real details:
8/24/2011 2:55:26 AM   General Exception       AssemblyVersion: -1; PortalID: -1; PortalName ...
AssemblyVersion: -1
PortalID: -1
PortalName:
UserID: -1
UserName:
ActiveTabID: -1
ActiveTabName:
RawURL:
AbsoluteURL:
AbsoluteURLReferrer:
UserAgent:
DefaultDataProvider:
ExceptionGUID:
InnerException: Unhandled Error:
FileName:
FileLineNumber: -1
FileColumnNumber: -1
Method:
StackTrace:
Message: System.Exception: Unhandled Error:
Source:
Server Name: ADVANCEDHIRING

I may have inadvertently caused my problem with DNN File Manager not recognizing the files

I was using Windows Explorer to move the file into the folder, not FTP. (I thought it was essentially the same thing). Turns out that using FTP DNN sees the files after doing a recursive synch.

Thanks for all your help Cathal!