I'm having an issue where whenever I export an H.264 directly from FCP it will only export from 0:00 to 1:30 regardless of where my In and Out points are set. I've had this issue in multiple sequences and projects.
Unless there is a reason you need to go straight to H.264, export the sequence at Current Settings and convert that to H.264 using either Quicktime, Compressor or MPEG Streamclip.
That way you can at the very least the sequence delivered, and trouble shoot during the encode.
In response to your question though, I have had dodgy luck at best using the QT conversion export in FCP. It does a much better job of spitting it out how it was cut. Which then allows you to easily convert to something else. In some cases, going to the intermediate then compressing can be faster than, or at least comparable to, doing in one step.