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Hi Matt
I suspect possibly browser or server caching could be the reason for the disappearing errors but could be wrong about that.
Regarding versions to export there's no one size fits all here. In a test course try exporting and importing the same LO as both 1.2 and 2004, then interact with the LO as a student and look at the tracking results as a teacher or admin. You'll see quite a bit of difference between the two versions but might decide 2004 shows too much in too may rows compared with the earlier 1.2 report. Both should work but personally I prefer the longer more separated results from the 2004 export.
You should also think carefully about what to export and what to simply link or embed from your Xerte install. Linking or embedding makes it much easier to keep resources updated and improved and fixed if there are changes to external services like YouTube or Mathjax etc. If you want to track quiz scores consider creating the quizzes as separate LO's or just linking from a Xerte LO to a moodle quiz and then from that back to the next LO. Although a bit old now referring to an older version my previous screencasts cover that in a bit more detail mitchellmedia.co.uk/xerte
HTH
Ron

Cheers Ron that's a great help. I'm sure it won't be my last issue I have!
Many thanks again.

Matt