Installing by cable with 'javaloader -usb load app.cod' works fine, and the app runs on the device with no problems, as on the simulator. The cod is using restricted APIs, but it's signed. The alx is a trivial nearly-empty one generated by JDE 5.0.
Despite all this, trying to load it onto the device (BB 8900) in the applications section of the Blackberry Desktop Software says:
'There was an error importing files. No additional applications can be found. Your file might contains applications that already exist in the application list, are not compatible for your device, or have errors'.
I quite need this to be installable with users' standard tools. What can I do about this? Is there any way I can get the desktop app to give me more information?
Not really enough information to answer but on potential cause is the version data in your ALX. If you have not removed the application (using javaloader) before trying to install with Desktop Manager, and the version information in the ALX is not higher than the module version data the software won't install.
There could be other problems, but without the acutal ALX, and the OS version information for the device it is difficult to say what they may be.