A few things:
Since you are getting sound from the TV, your HDMI signal is working all the way through (the 990's DVI switching is passing the audio from the BD player to the TV). If you don't want that, you can either mute the TV, turn the TV's speaker volume down to zero, or disable the TV's speakers entirely. (I usually do the latter since I never use my TV's speakers.)
When you connected the analog audio cables from the Samsung player to the 990, you are using the 7.1 Direct input. Your DVD player was almost certainly configured on a different input (DVD most likely, or maybe one of the Video inputs). You will need to assign the DVI input (DVI1 or DVI2) that you are using to the video source for the 7.1 Direct input, and then you'll need to select "7.1D" on the remote instead of the other video input you were using (DVD, most likely). At that point, you'll get the audio from the player to the 990 over analog.
If none of that helps, please let us know. Many of the tips in my
990/BDP-83 setup guide also apply for your Samsung player and the 990, so that page may be a useful reference.