I'm no expert on this but have learned the hard way (and by asking, as you have) and managed to fix pretty well all the problems both downloading and uploading but, sometimes, we just have to pick our brains as something comes up when the actual files or site can't offer a reason for why somethings going wrong.
From what you say, parts of the file are going missing when you start to redownload (hence the difference in downloaded and the actual size of the file) so instead of the 95% you had, you now only have 30%.
Just as a thought, are you downloading to an external drive(s)? I had that and the drive letter changed and it caused all sorts of problems. There were bits of the torrent all over the place :
That meant that I started the download on, say "F" drive and the next time I switched the PC on it decided that it was now "G" drive and a second external disc was now the "F" drive, and so started downloading to that one (from the start). Next time it reversed them and started downloading to the first drive again (but showed a lower % as yours did).
As the files are so large and you probably don't get them all in one go, I suspect that something like that may be happening each time you swithch the PC on.
That's the sort of thing that causes these problems so you really have to search around and see what's happening on your own machine.
I'm sure there are hundreds of variations to that theme so it's a case of sitting in front of the PC and thinking hard. It'll come to you in a flash, I'm sure.
As I say, I can't think of anything with Mousebits that would cause it. ???
Hope you get it sorted out.