Correct of SCP command on Ubuntu Hardy

That should absolutely match hidden files. The / at the end of the source says "every file under this directory". Nevertheless, testing and research bear you out. This is stupid behavior.

The "answer" is to append a dot to the end of the source:

scp -rp src/. user@server:dest/

The real answer is to use rsync.

One of the easiest ways to get around character escaping on the command-line (if that's the cause of the problem) is to use tab-completion to let it fill in the "awkward" characters; depending on how full your /ReferenceFiles directory is, you might be able to do something like

  scp -P portNumber /Ref<tab>CompanyA<tab>Some<tab>Game/file user@server:...

Alternately, you can use a ? instead of a character, provided there aren't going to be too many conflicting file/directory names:

 scp -P portNumber /ReferenceFiles/CompanyA,The/Some?DirectoryWithA?Space/Game/file ...

For directories, you need to use the -r option to scp (its omission is why you got the "not a regular file" error).

Lastly, could it be that the destination on the server doesn't exist as typed, and that's the source of the error (and not the source file)?