Its caused by the CD DISC manufacturers not sticking to "the book" (usually deliberately to try and confuse CD-ROM drives on PCs as a very basic Anti-piracy stunt).
I used to have this problem on various pre-80minute CDs CD-decks and also on my DN-D9000 - but not anymore.
What version of firmware is in your DN-D9000 (It'll be displayed on the screen when you go into presets)? Its quick, easy and free to update the firmware on a Denon, unlike on say...(as mentioned above)...a Pioneer, who have previously made users send their CDJ's back to the factory for the numerous firmware upgrades to allow their earlier players to play CD-singles without stopping randomly, play CD singles with video tracks on them, accept CDR's over 74 mins long etc. Indeed, someone who bought a CDJ-1000mk1 at time of release would have had to have had to have returned their CDJs' for firmware upgrades 3 times (4 firmware releases...version 5 went straight into the CDJ1000 mk2...to find out Pio firmware version, hold down "Loop out" for 5 seconds).
On Denon's you can download the latest firmware free from the website (you'll need your serial number from the label on the back of the unit), burn it to CDR, insert that disc in your Denon, and a couple of minutes later - you've got the very latest firmware in your pride-and-joy.
Tonsk, PM me with your firmware version (from the Preset menu)...cheers!