I have found the exact same problem, only 19 of ~100 caches downloaded are displayed.
I agree that it would have been nice for this to have been mentioned in the manual (or even online!!)
Also found that if I download the geo-caches as simple waypoints that it will only displaying 19 of them as well. Must admit I am a bit disappointed with this :-<.
Glad I found this post to help explain it.
Thanks
Teammac5