Regardless of how the PDF was generated (it could have been done on a VAX 11/780 for all I care) I still don't see a mechanism for fonts being the wrong size on the first download, and being magically fixed on a second download.
The PDF file is the same
It has to be a client side issue.
Ever wonder why some websites show a crypto hash and/or signature next to the file they make available for download ?
Two words....file corruption....
If you don't have a hash or sig available to check against, then you've no way of knowing your download was good. Hence, if you suspect something's up, best thing to do is to try downloading it again (perhaps on another day on another internet connection).