Sorry to say that I spotted the problem right away...You made a rot cellar and that is just what they are doing...

As mentioned in many previous threads, a dip into water and chlorine bleach can kill off most surface mold before it starts doing damage. A gallon of water mixed with a couple of tablespoons of bleach will work well. Allow it to remain without drying or rinsing it off. The dip would be for about a minute to two.
You had a slip here too:
"I made a rot cellar in my garage" Rot?? no, but in your case, yes..

There is no way to stop its damage now, and those that are rotting even slightly, simply peel, remove rotted surfaces, cut up in chunks and freeze.

Hmm, do the moldy ones have any nicks or cuts in the skin?

I store my B-nuts with whatever dirt they came in from the field with, some are quite dirty, others very clean. I have had some start to go bad, I have noticed that these are ONLY the ones that had a cut in the skin. So I always choose squash that have nicks in the skin and use those first, since they don't store as long as the unblemished ones.

My storage is a closet that is usually mod 50s, I didn't choose the temp, that is just what it happens to be so I don't know if that is good or not.

I also wonder, is there any possibility your root cellar got below freezing and they slightly froze and then thawed?

haha forgive me that was a joke I couldn't resist.

Even though they are quite hard, most squash bruise easily, so use care in handlng and don't stack more than two on top of each other.

It might be worth measuring the humidity in that "root" cellar for future reference. Some things like more humidity for storage than other things. I'm in Florida so I can't really make any sort of root cellar without a walk in refrigeration unit so most long keeping produce gets to enjoy living temperatures for as long as it can (at least sweet potatoes keep relatively well that way for a while and are still quite edible even when they sprout.)

Good Luck!

I have my B squashes in a sort-of-cellar, pre-rinsed in a light chlorine solution. They aren't getting moldy or "bad", but the flesh isn't quite what I had hoped it would be. I'm a bit disappointed. Maybe refrigeration would have been better.

I wonder if the clorine bleach solution works. I picked about 30 butternut squashes in the fall last year. I stored them all in my spare refrigerator. Half of them I put in with no washing, etc. Most of these didn't mold, and lasted about 3 months. Most were eaten within this time. Only two got moldy. I washed the other half in a mild clorine bleach solution. They all went bad within 3 weeks.

Thanks for all the help.

Anyone try vinegar diluted water besides bleach for a wash?

I think how well squash keep varies a lot from year to year based upon the growing conditions as well. We had a LOT of rain in September this year (8 inches), and it was cool and wet most of the season. My squash didn't keep nearly as well this year as they have in many past years. I've often kept butternuts in my basement for up to a year, but this current crop all started going bad in Novemberish, and I processed them from time to time, finally doing the rest of them in January. So, they're now frozen and ready to use, which isn't all bad, either.

Dennis
SE Michigan

I tried keeping squash in a root cellar for a few years, and they always started to go off about now - late Feb - March. Now I keep them in a sunny, airy, dry room, and they'll keep until April - May, when it starts getting too hot in there.

They do dry out a bit, get just a bit wrinkly, and the natural wax protective coat starts to really show as a white, flaky film.

And my, to they make great pies, about now ....

Vinegar isn't as effective unles they get at least a 50% mix of it with water. If you don't trust chlorine, consider its something that eventually evaoprates and leaves no real traces behind. Same in swimming pools where the sun makes it go away. Another option is to use sulfur and water mix, like sodium or potassium metabisulfate. These are used as soaks for sliced potatoes that are to be dried. It prevents oxidation and also kills mold and while yeast spores. The sulfur is used in many wine making processes and is also used to 'sanitize' the barrels it may be stored in.

I much prefer the buttercup types (Kobachi, sp.) as its sweeter and richer tasting and lasts quite a long time too.

I have a spare refrigerator in my barn - Can butternut squash be stored in there since here in LA we will not see 50 degrees until Oct/Nov?

Feb. 10, 2021:

I have successfully stored butternut squash for years in our crawl space after a light wash in water with bleach. This year it ripened late, and some were not fully pear shaped but round. The color was right so I picked them. A lot of the round ones and some of the pear shaped ones now have deep wrinkles in the skin. Any ideas why?

Kasm

Kasm, if they are in storage for long periods of time they start to dry out, and they become stringy. I've still got several crates full back in my storage and a few that I've cut have become fibrous in the middle. I just scrape that out along with the seeds and proceed like always.

I've been sorting through mine periodically, usually I bake them and freeze the pulp but I just don't have a lot of extra freezer room this year. My local food bank has been happy to get them, so they aren't going to waste.

I picked them last September and so they've been in storage for 6 months now and most are still good, but a few have spoiled, so I see the writing on the wall.

Annie

I'm just chiming in to say I think having a "rot cellar" is the best Freudian

Slip of all time!
That's definitely what it would be for me!
LOL
Carla in Sac