Managed to answer my own question, though I'm mildly worried as to future updates and such.
I managed to get the site to upload correctly by uploading a .swf with a completely different filename.
previously I had been uploading wractive5.swf to the server.
then renaming the already hosted wractive.swf to wractiveBackup.swf.
then renaming to wractive5.swf to wractive.swf
this should work as I've done it before on many servers!
however I uploaded a siteVersion59.swf then renamed to wractive.swf and it worked.
after that I retried wractive5.swf and that worked too.
strange but true. I'd ask the support team to look into this as it is not ideal and there appears to be serious issues regarding your ftp. I've never been disconnected so many times either in one session.