Hi DJay,
I face the same issue as you. My DNS-323 is currently v.1.07 and when I add new videos to DNS-323, the PS3 is not able to list the new videos. However, it is able to display the old videos. Even if I did a manual refresh in DNS-323, the PS3 still does not list the new videos.
The weird thing is after a few days the PS3 list the new videos. I had not faced this issue in the earlier firmwares (v.1.04 if I recall correctly).