Seriously I have no idea what you are doing but this totally does not happen. (Update: Wait, I think I've figured it out... Hmm... See end.)
Please follow these identical instructions exactly. I'm doing this now on qa.moodle.net which is publicly accessible so you can do it on that server too (but it does also work on 2.1.x which we still use at the OU).
1. Take two image files which must be called a.jpg and b.jpg.
2. On qa.moodle.net, log in as manager.
3. Go into the course 'Moodle features demo'.
4. Turn editing on.
5. From 'Add a resource', choose 'File'.
6. Type in the name 'Predictable file URLS - the definitive proof' and type 'x' in description.
7. Under content, click Add and choose File upload. Browse to a.jpg.
8. OK everything (we're going to close it down to prove you can add files later) and click 'Save and display'.
9. On the resulting page, right-click the image and choose 'Copy image location'. Then open a new tab and paste in the URL, which will be something like:
http://qa.moodle.net/pluginfile.php/179/mod_resource/content/1/a.jpg?stopthedamnfilter
10. Back in the Moodle page, choose 'Edit settings'.
11. Click Add, upload a file, browse to b.jpg, save and display (resulting page still only shows a.jpg)
12. In your other browser tab where you had the image open on its own, change the URL to b.jpg without changing anything else:
http://qa.moodle.net/pluginfile.php/179/mod_resource/content/1/b.jpg?stopthedamnfilter
13. Observe that the second image loads and none of the numbers changed.
OKAY, here's the part where I finally figured it out. What you're trying to do is add a whole directory of files to a File resource at once by adding a single file. As you say this doesn't work. If you want to achieve that, you can do so by uploading a zipfile and expanding it. Another way (if you want it in multiple places) would be to ensure you manage these files within Moodle as a File object so that this is the definitive location. For example, you might want to put it in the front page site files area so that everyone can access it, or otherwise put it in a course that you know all necessary users can access. (Hint: Metacourse.)
Within a File object, all added files have a predictable URL. This means that by adding and using a single File object you can have identical feature to that provided by the 'Files' section in Moodle 1.9, the difference being that it's now possible (not mandatory!) to have multiple File objects in a course instead of just one. As before the URLs are entirely predictable within a File object but they are not predictable between File objects due to the inclusion of different numerical identifiers (in the case of Moodle 1.9, it's course IDs; in Moodle 2 it's context IDs). So there has been no reduction in functionality in this area since 1.9.
I believe in 2.3 it is planned to have repository support that will let you share files in lots of different locations (e.g. let's say you want 10 copies of your 'here are all the files' object because you don't want to put it in front page files for some reason [licensing, etc] but you need it on 10 different course - at present, just like in Moodle 1.9, this would require 10 independent copies of the object and if you edit one the other 9 won't change - in 2.3 there is supposed to be a way to defer this to an external repository or otherwise allow you to update the file once and change it everywhere).
--sam