TC accurate edits during conversions

I'm at a facility that does a ton of work using the the Kona 3. One of the gotchas we're consistently running into are TC accurate outputs when doing any type of conversion with the card. Here's a prime example:

Timeline is 720p 23.98 (DVCPro HD, 8bit, or 10bit, doesn't matter). We need to output to HDCAM at 1080i. So, FCP's playback is set to 720p 59.94 (this adds pulldown to the 24p timeline). Then the Kona is set to cross-convert to 1080i 29.97. The outputs work and look great. The issue is that 9 times out of 10 the output is a field off. If my first frame of picture should be at 01:00:00:00 it may land on that frame, but on the second field instead of the first. Changing playback offsets only moves it an entire frame ahead or back, but it still lands a field late.

What is going on here? Anyone else experience this? I've tried locking to difference references because I'm in a big facility and have a lot at our disposal. All to no avail. Sometimes it works, sometimes doesn't.