I never had this problem in X1 or even way back when I used Music Creator, but whenever I try to export a mix the first few notes are always missing. I've read threads where people have issues with MIDI missing at the beginning of a song, but never audio. I suppose I can simply start the song at measure 2 to avoid this issue but are there other workarounds? As much as I've enjoyed working with X2, I'm a little surprised such a basic feature has this issue.

I'm guessing your project starts at 01:01:000 yes?
 
Try inserting a blank measure and as you say, export from measure 2, see what happens.
 
You're correct in saying the Sonar has historically had a problem "grabbing hold" of the first couple of Midi notes if they're at 01:01:000, but I've never heard this happen with audio before.

Export works on the selected region.. If you do not select the first measure it will not be included. Try control a before exporting.

I always use the first 2 measures for count in..... and the song "officially" starts at M-3 not counting any pickup notes.
 
Be sure the entire song is selected for the export. I have messed up a time or two and missed some things in the export by not having the entire song selected. I double click the tracks a few times and they cycle through selection of clips, tracks and all tracks..... I stop on ALL TRACKS.
 
I get the entire project, including the count in by doing this.

I've seen this behavior, too. I had a song that began at zero after replacing my usual 2-measure count-in with a drum intro. The first hit would start playing a couple milliseconds in. I tried to work around it by pasting a hit from elsewhere in the drum track, but no matter what I put there that first note came out distorted.
 
My solution: I nudged that first hit back by a few milliseconds, not enough to notice the timing error but enough to overcome whatever bug causes it to be truncated. Experiments showed that the amount of time needed to avoid the issue was about equal to one buffer-full of data, e.g. 12ms for a 512-sample buffer @ 44.1KHz.
 
Nowadays I routinely leave a 4-measure lead-in of silence, just in case I want to insert something there later.

Are you using any thirty two bit plugs? Perhaps enabling and disabling all effects prior to bounce might help?