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I'm receiving the following error message in the log (qbittorrent-nox.log):

An I/O error occurred, '<torrent name>' paused.
Reason: <torrent name> file (/home/jake/Downloads/<torrent name>.!qB) error: Permission denied

The torrent will download some data, and then error out.  I can resume the torrent, and QBT will download some data, and after an amount of time, the error will reappear.

I have other torrents that do not have this problem.

ls  -l
drwxrwxr-x 5 jake jake    4096 May 19 19:28 <torrent name>

Pre-allocate disk space for all files = Yes
Append .!qB extension to incomplete files = Yes

qBittorrent v3.1.11
Lubuntu 15.04

[Solution]
One of the files for the torrent had a different owner/group (root) and permissions.  This was found in a subfolder of the parent torrent.
I changed the file owner/group and permissions to the account the service uses.

Putting 2 and 2 together;

One two being this thread  and the other two being that thread >> index.php/topic,3526.msg15523/topicseen.html

Yes, it could be because your 'home' folder is encrypted.

is your download location in your 'home' folder?

I now have an unencrypted the folder.

I'm suspicious of what happens when I disable (remove a checkmark) from the content tab to not download a file, and then I re-enable the file.
I wonder if QBT plays around with the permissions, and doesn't add permissions when I re-enable the file.

I wonder if QBT plays around with the permissions

It doesn't, the files will / should  inherit the permissions from the folder structure.

I know this is regarding Linux, which I don't use so this might not be the answer you seek, but the one time I encountered a very similar error was because the overall length of the path name for one of the files in the torrent I was downloading was longer than allowed by the OS (Windows NTFS in my case, which is 256 characters maximum including the drive letter, colon, and backslash). I had to choose the root of my drive instead of the folder I usually use for all my torrents, after which it downloaded just fine.

Solution:
One of the files for the torrent had a different owner/group (root) and permissions.
I changed the file owner/group and permissions to the account the service uses.

Not sure how this was caused.