I too have had this problem with my email provider, a local ISP in the Calif Gold Country...
I noted that the blank messages were always grouped as a thread.. so, I went to settings and turned off "Organize by Thread", and re-checked messages. Each of the "blank" messages showed up as actual messages. So, I'm guessing it is a bit of bug with the "organize by thread" option.
I turned the option back "on" and had no odd blank messages.. We'll see if this persists or the turn off then on option needs to be done again.
DonnieC