Why are my database files (.dbf) updated but not the cubes (.mdc) ?

Answer: The cubes are not run/downloaded properly.

(assuming you have scripts to run the cubes)
Double check if the date of the cubes is as at current.
Else do the following :
To click and run the script again - manually
How to run manual:
1. Cognos Powerplay Transformer
2. Open "...... .pyi" (Usually the name is the same as the one in .mdc, just that you have to open the corresponding .pyi file)
3. Click on the cube icon to run the cube.
OR 
If you have scheduled a task to run the script automatically (which will run the cubes), then you might also wish to wait for the next update (depending on your scheduler: Control Panel > Scheduled Tasks) and then check if the cubes are now updated.