Having read everyone's contribution, I have to agree that infection alone should not account for such considerable loss of alcohol. I would look for errors in process as well. I am a big fan of the old "idiot check". Does the drain valve on your still leak? If you can, borrow a FLUER look at your still and see if you have unexplained thermal venting that would indicate a leak? Is your condensed product cool enough that it is not volatilizing and evaporating in to the air? Are your helpers somehow losing product? Retrain and reconfirm SOPs. I call it an idiot check, but sometimes we cant see the forest for the trees. I was noticing a loss in production and found the culprit to be a leaky butterfly valve at the bottom of my spirit still. Because of a worn out $20 gasket, I was literally letting my hard work and profits leak down the drain. Another time, I watched an assistant let the alcohol between gaskets fall on the floor when disconnecting hoses. I had to explain to him that those 'pennies' will make or break a small distillery and he is to use a drip pan. Try to look at your process with someone-elses eyes and look for the things that you are too familiar to see with your own eyes. Maybe ask a local friend in the industry to come and look?
I dealt with a nasty infection a while ago and to finally beat it we had to go nuclear. I pumped live steam through every single vessel and piece of equipment that has contact with any part the process. I replaced each and every gasket, took apart my heat exchange and sterilized all parts replaced any serviceable parts. It was expensive- and a pain, but we finally beat the infection, and in the end that is cheaper than compromising your product. I am also a fan of regular sanitation as part of your process, all of our fermentation and holding equipment undergoes brewery style caustic, acid, and sani CIP on a regular basis.
You are on the right track, just apply the scientific process and eliminate one factor at a time. I think in the end you will find that it was a number of small culprits conspiring to create one big problem. Do a few plates to see what you are dealing with, that should speed things up.
Good luck!