Hey guys, believe this is a known issue with ID #45804 and has a status of fixed and therefore should be part of the upcoming version 10 SR5 release as far as I can see. Hope this helps.
The workaround would be to use a supporting task\external program via Publisher to run a QV.exe /r on the QVW(s) that need to get to the FTP site, this should take care of things until the fix is out for the QDS.
I've been confirmed this is a bug ID 45804, that will be fixed in the next SR5, the Work around is as Brett Bleess previous post, if you extremely need the SR4 before SR5 Release and want to fix this you should contact Qlikview Support.
We experienced similar issues with HTML downloads after an upgrade to 10 SR4 from 10 SR3. The workaround recommended above works around the issue (although not particularly practical if you have a large number of documents!). Slightly concerning that seemingly core functionality like this isn't picked up in testing before the release.