[nzbget] NZBget 0.7.0 download and discussion

[Lurch]

Have looked through this thread and haven't found this question, hope I haven't missed it, but here goes.

I still often download nzb files manually and copy them to the nzb directory via FTP, where NZBGET then picks it up and starts to download.
Now initially the nzb direvtory was /share/.nzbget/nzb/
Installing a newer release via CSI changed that to /share/Apps/NZBget/.nzbget/nzb/
so I changed the bookmark in my FTP client to match.

Now a few days ago I use CSI to upgrade to the latest version, and now that bookmark doesn't work anymore, browsing through samba to the directory reveals that it's gone, although the FTP client shows a linked folder (but trying to open it as no effect).
Checking the config of NZBGET through the web interface shows that that should still be the correct folder.
A bit more clicking around reveals that nzbs are now being dropped in the old location again (coming in from TVNZB for example)...
/share/.nzbget/nzb/ even though the nzb directory according to the settings is /share/Apps/NZBget/.nzbget/nzb/

I'm a little confused.
Can someone explain this or clarify the logic?