How to replicate (for this example):
Default download folder = E:\DL\In\
Category folder = E:\DL\CategoryFolder\

1. Add a big torrent, assign it a category with it's own folder (E:\DL\CategoryFolder\ in this example)
2. Select just 1 (or more, just not all) file(s) to complete with all other files set to Priority 'off' to not download
3. When download finishes, download is properly where it should be, E:\DL\CategoryFolder\ with just the 1 file completed
4. Now select the rest of the files to priority normal (doesnt need to be all of them, just something to download)
5. Start download, making it allocate/download the rest of the files in the torrent
6. When download completes, instead of being in E:\DL\CategoryFolder\, now the downloaded files lie in E:\DL\In\

Yes, thank you! I've noticed this odd behaviour many times and it's causing me a lot of pain as you can read below.

So to confirm what the OP wrote, my settings are something like this:

Default downloading location:
E://Torrents/Downloading

Default completed/seeding location:
E://Torrents/Completed

Completed/seeding location for "TV" category:
E://Torrents/Completed/TV

When first downloading a torrent containing many episodes or seasons, I select only a small number of episodes and start the torrent, for example episodes 1-5. During the download, the torrent files are correctly stored in the default downloading location and when the torrent(selected episodes) completes downloading, the episodes are moved to the correct category seeding location...

E://Torrents/Completed/TV/Show_Name/...

The problem occurs when I go to download additional episodes, for example 6-10. I select those episodes and change their priority from Off to Normal and start the torrent once again. Now, instead of the downloading episodes being stored in the default downloading location, they actually appear in the category seeding location!

So instead of the incomplete/currently downloading episodes being stored in...

E://Torrents/Downloading

... they are improperly stored in...

E://Torrents/Completed/TV/Show_Name/...

Not only that, but once the additional episodes do complete downloading, all the completed files move out of the correct category seeding location...

E://Torrents/Completed/TV/Show_Name/...

... and into the incorrect default completed/seeding location...

E://Torrents/Completed

The biggest problem for me with this, other than files just not being where they're supposed to be, is that I have software that monitors the category seeding location for newly downloaded episodes and then renames, sorts and stores those episodes on my NAS. Because Tixati places incomplete/downloading video files into the category seeding location, my software grabs a bunch of unfinished video files and moves them to my NAS which I then have to clean up.

So yes, please please please figure out why tixati is moving and storing files in incorrect locations.

Thanks!

Ooops... all my E:// should be E:\ ... Apparently I'm spending too much time on the internet. hahaha