File download "save as" function doesn't work correctly

I am using Firefox 24.3.0 ESR on Linux LXLE 12.04.3. I have problems downloading some files from some sites. After some investigation I found that the files have been given the generic MIME type octet-stream by the server. Presumably this is to encourage me to download the file rather than have it open automatically in the browser.
For instance, if downloading one of these files that is a pdf file, left click gives me the standard box that allows me to choose to open the file in the default application or "save as". Once I do the left click, I can see that the file immediately starts to download in the background (network activity). If I wish to open it in the default application, it works. The green download arrow flashes and eventually the default application opens with the downloaded file when the download is complete. The download is then listed in my download library.
If I select "save as" and my preference is set to download files to a fixed directory, it ignores the directory they should go to and places them in my home directory. The green download arrow flashes and again records the download in the download library.
If I set the preference to "always ask me where to save files" then when I click on "save as" nothing happens. The green download arrow doesn't flinch and nothing appears in the download library.
After hunting around I found that the file has actually downloaded to my /tmp directory. Clearly that was the background activity mentioned above. The name of the file in the /tmp directory is made up of seemingly random characters and I can retrieve it from there but this isn't exactly ideal and I would like this to work the way it is supposed to. i.e. I want to be able to click on "save as" and select where I want the file to be downloaded to (and it to go there).
What could be causing this behaviour and how do I get the "save as" function to work?

jscher:
Thanks. The /tmp and home directories are on the same partition as the main operating system. The Downloads directory is actually set up as a sub-directory of the home one but is a symbolic link to a NAS drive. It works fine for other MIME types. It is just when web sites use the application/octet-stream MIME type that I get this problem.
I checked the permissions and the /tmp and Downloads directories have full read write permissions for everyone. The home directory is the one with the restriction that only I can write to it.
So, I don't expect that sheds any light on the problem.
cor-el:
Thanks. I meant to say in my first post (but pressed the button before it got in) that I actually created a completely new Firefox profile and the problem is still there. Sorry, I should have included that.
The only difference with the fresh profile is that the "open in default application" isn't available, presumably because no default application has been assigned. The "save as" behaviour is still the same.
So, if the problem exists in a pristine profile, it looks like there is something deeper wrong.

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