When I render files using After Effects CS 5.5 with timecode support I get a resulting file with inaccurate timecode. My source material is Arri Alexa ProRes Files & Canon EOS Camera Files, both 23.98. When imported into After Effects they show up with correct timecode and frame rate. Once files are rendered out of After Effects and imported into Final Cut Pro or opened by QuickTime Pro they show up as 30fps and the time code is shifted. However if I import the rendered files back into After Effects they show up correctly in the browser.
I have it set to "Timecode - > Use Media Source". However, the link you provided says "Important: Changing the time display format does not alter the frame rate of your assets or output—it changes only how frames are numbered for display in After Effects." So I'm not sure where the issue is happening.
If Adobe is in fact aware as Dave says, let's hope they solve this asap. Nothing more frustrating that a great new (overdue) feature that doesn't work as expected.
I'll update if I find a workaround in the meantime.