I'm going to try and explain this as best as possible:

I'm working with the XDCAM Ex 1080p24 (35MB/S) codec in a 23.98 timeline, 1920x 1080 in FCP. I have the computer hooked up to an Sony HDW-D1800 through an AJA Kohna card.

I'm trying to output my timeline to an HDCAM tape. When I playback my timeline with no tape in the deck, it works perfectly. Playback is fine, and it plays back perfectly in the reference monitor as well. Once I pop a tape in and try and do a record, I loose all playback through the deck. It's playing in FCP, but failing to record to the deck. When I play back the tape, it has a few random frames from the timeline on it, but obviously not the actual sequence.

I can import clips perfectly.

In the AJA kohan control panel SDI in is 1080sf23.98, buffer is 1080sf23.98 and SDI out is 1080sf23.98.

The system frequency on the deck is set to 23.98sf, Pull Down (SD)

And in FCP my device control preset is AJA Kona LH: 23.98 Sony VTR
and playback is AJA Kona 1080psf23.98 8 Bit 1920 x 1080

I tried to post all the information I have. What am I doing wrong?

I'm assuming your using Edit to tape and your 9 pin is connected and the deck is on remote. Double check to make sure you are in Mastering for the Edit to Tape tool along with choosing assemble edit when dragging over your sequence. If all of that is set correctly make sure in the bottom right corner of the Edit to tape tool all of the icons are yellow: Timecode, Video, and all the necessary tracks of audio. Also be sure to pick VTR A in the settings since that will lay down VITC as well as LTC. VTR B doesn't for some reason.

Does the layback fail in FCP or is the deck just not getting a signal but FCP is going about it no problem?

the problem has been solved. In the AJA control panel, we checked the Gen Lock setting. Video In was selected (which, I believed it should have been), however we changed it to Freerun, and now we can crash record no problem. Edit to tape still does not work though, but as long as we can crash record, we're okay.

Edit to tape took me a while to get used to coming from Avid. Also dealing with third party hardware also made it rather difficult, that is why the AJA control panel is in my genie bar for quick access.