I have been using Tixati for a while. It's a great torrent client. But the ISO's I downloaded by Tixati can't be mounted by built in Windows Explorer in Windows 8.1. So I did a little googling & found out that the download manager is setting the download file to be a sparse file. The work around of this problem is to copy the file & it can be mounted. It is very time consuming to copy a large file again & also very annoying.
I hope you can fix this problem as soon as possible.

So is this a fragmentation issue?  

Have you tried the other file allocation settings?

Settings > Transfers > Local files > File allocation : Full Pre-write.

I am not aware of a setting location Per torrent, but you can change it before adding an iso torrent then change it back to sparse for other torrents.

Another work around could be to use a disk defragmenter such as the free Defraggler from piriform. It will defragment a single file if so desired.