Hello,
it would be very helful if you could closer specify the "sometimes".
When does it work and when not?
Do you have any other SEO tools installed or plug-ins (mambots) installed?
Basically, JoomSEF will set the meta values and unless overriden by something else, they should be generated. So if it works "sometimes", it seems that in other cases, the meta produces by JoomSEF will be overriden by some other piece of code.
To debug this, if you have multiplme plugins (mambots) on, try to swtich them off one after another to try to find out, what might be causing it.
Best regards,
Michal