We would need to know how to reproduce the issue reliably using out of the box installation. There are too many unknown variable to us - the front end project is completely unknown, environment as well.
If it works sometimes and also if there is another form which works, it does not seem to by a system, Kentico issue. I would focus on what is different. Is the form placed on a different page? Is it used different times during the day? File format you mean the same file extension? What is the content of the missing files? IS there any suspicious content which could be blocked by some security tools? Any pattern or any difference can give us some hints.
I would also try restoring the backups on other environment - this can tell us also whether the issue is environment based (e.g. some security setup is blocking certain attachments) or, it is for example web farm sync issue, code issue in the project (event handler code, etc. ) - we will at least know where to look further and it will limit the set of possible causes.