This turned out to be space issue, as I didn't know it copied to a different location when uploading, then moves it into the DB, then to the jds so for large files you need space in 3 locations....

It was then failing as the DB was 'dirty' so a clean up fixed that.

I'm having the same problem - were there specific locations you needed to add space to?

Yep, there is a few locations actually (unfortunately). Firstly it uploads to your tomcat temp, if using the default install on linux its here /usr/local/jss/tomcat/temp, it then puts this into the database, so wherever your db is will need the space as well, then finally it copies into your JDS /tmp dir, there is a feature request to be able to change this https://jamfnation.jamfsoftware.com/featureRequest.html?id=1886

Then from your JSS if you go to computer management, JDS, then change to grid view you can see how the propagation it going to your JDS's. Once its complete best to do a bit of clean up on your DB, something like

mysqlcheck -u root -p --repair --optimize --databases jamfsoftware

Good luck with it