What operating system? Server= 2003, SP2, IIS6, .NET 4.0, Test machine=Win 7, 64 bit, SP1
What database platform? MS SQL Server 2008
What version of mojoPortal? 2.3.9.7 MSSQL
What version of .NET? 4.0
Steps to produce the problem, expected results, and actual results:

I have tested in IE9/10, Firefox, and Chrome. I am updating a couple test sites but also setting up a fresh new test site.

1. I go to Administration, File Manager (I default to alternative manager that has the new "drag and drop, multiple file selection and a progress bar in modern browsers" - /Admin/FileManagerAlt.aspx).

2. Click Select files... button, and choose one small (111kb) .jpg file in the pop-up "File Upload" window, and click Open.

3. Returns to the File Manager, puts progress bar beside Select files... button, removes Upload button, and gives "Oops something went wrong uploading, you may want to contact the site administrator an error was probably logged."

No file is uploaded, and System Log shows "2013-07-17 17:10:58,538 INFO 10.2.1.200 - en-US - /Services/FileService.ashx?cmd=uploadfm&t=8813bdf8-8895-4486-a514-0828532d6dde - mojoPortal.Web.Services.FileService - returning 404 for upload request to / "

For the server/file permissions test, I can successfully upload using the TinyMCE HTML content editor Insert Image function. I can also use the "other" file manager (/Admin/FileManager.aspx) to upload one file at a time. So that tells me the permissions are ok for writing access, and that the log file is getting the error written as well. Also, I'm the only user right now, and as such am also an administrator. So the new file uploader is not working for me, in any of the 4 mentioned test browsers.

Thanks in advance for any help!

I admit I use F12 (IE and Firefox's Firebug) mostly for the HTML tab (style, layout, etc tweaking/review). I've not used the Console or Net tabs. So I'm not sure what to look for, but what I'm seeing I'll put below. If it helps, and I hope it does, I can reproduce this on your demo site now.

Also possibly more helpful, to answer your second questions - it is in the default folder when you go into the Alternate File Manager: ~/Data/Sites/1/media/. I did try a sub-folder, and it does successfully upload. Ironically if I click to view a sub-folder and then go back up to the main/default folder (~/Data/Sites/1/media/) I can successfully upload then as well. So to clarify, this happens if you go into the Alternate File Manager and attempt to upload to the root/default directory without doing anything else. (Again, after this testing, I went to your demo site and after clicking to get to the Alternate File Manager and attempting an upload in that root/default I can see the error there as well). I don't think I can attach any screenshots here to help, but I hope that I've given enough info that you can reproduce on your side.

Errors that Firebug is showing in Console or Net: "NetworkError: 404 Not Found - https://jnf.visualsolutionsinc.com/Services/FileService.ashx?cmd=uploadfm&t=d76cbd6f-cef5-406e-a698-47e886536ccf". Looks like in the Console I can expand the Post error and I get tabs for: Params, Headers, Post, XML, and Cookies. Let me know if you need any of this details sent. Probably easier for you to see it yourself and dig around using these tools - so hopefully you can recreate on your demo site like I did. Let me know though if I can provide anything else to help!

Least I can do. Glad the report and the steps made sense and were able to help get it resolved. Thanks for ALL you and the others here do as well, making this awesome software available and the forums!