Is not enough to upload the flash in the correct directory; you must modify the .thm file.
Folow this tutorial:
Part 1
After you've downloaded the Flash Menu/Theme (ZIP) and extracted it...
1. Launch a2uploader.exe
2. Click "FileSystem tool"
3. Power down your phone, remove and restore the battery
4. Connect your phone to PC while holding the "c" key
5. Navigate by double clicking: /tpa/preset/system/desktop/flash
6. Add the new menu by drag & drop (you can add more files simultaneously)
7. Once the upload to the phone is finished click Shutdown FS manager, quit the program, unplug your phone, and you can power it up.
Part 2
This part is all about assigning the menu to a theme (THM) file. If you got the THM in the zip with the menu then this step is not needed, just copy it to the phone and activate.
You need to pick a theme you want to have this new menu. Once you've got yourself a theme file (in this example I'll be using Crystal theme that I got with the phone). The latest version of Sony Ericsson Themes Creator is needed to apply required modifications to the theme.
1. Launch Sony Ericsson Themes Creator and load the theme you are about to modify. Once you load it the warning message like this might appear
In that case click Yes. These are elements that define the look of Media Center, from some reason Sony Ericsson still didn't incorporate to the program.
2. Click Tools and select Edit XML.
3. Scroll down and add a line:
<Desktop_style Source="MenuName_desktop.swf" Type="File"/>
The Source must be the name of the menu you want theme to load. So... Replace the "MenuName_desktop.swf" with the name of your menu. Extension ".swf" is required.
4. Click OK, in the warning that appear click Yes
5. Click File and then Save. If Themes Creator cannot save the file it might be set as Read Only. (Right-click the file, select Properties, uncheck "Read Only" and click OK, then you'll be able to save)
6. Close the Themes Creator, copy the theme to your phone and activate it. The new menu should appear.
If it doesn't... Is your phone branded? Some branded phones can't display flash, some only cannot change menus (because operator has it's own layout and he doesn't want it changed). Solution: Unbranding.