the other two throws error as well, but those error mean very little to me
Well, they might mean something to others, but if you do not tell us what they say, how can we help?
From what you have described it would appear that your server is not fast enough to process the upload of the files. Anyway, we are not experts on servers, specially non-apache ones.
I suggest you try to upload some of these files via FTP and see it that works. (E.g. you can see the items in Zenphoto without problems.) That will at least isolate the source of the problems.