Hi guys, just coming into this Thread way back from May!
I don't understand why your onions go bad, nor why your onion juice goes rotten either. I sometimes have an onion go soft and start to rot when it is in the bottom of the bag for a long time in hot weather.
Can't comment on onion juice as I don't have or purchase.
The onions in the kebab, chopped and mixed into the meat? Or were they chunks of onion separate on the kebabs?
With thawing, the onions will be soft and sort of translucent. Very reminicent of being rotten, but they aren't. If they were separate on the kebab I can see why they would look so.
Perhaps next time you would be able to purchase the meat separately, already mixed and ready to put on the sticks. Then you could add fresh onions inbetween.
If they are mixed into the meat already, then don't worry about the translucency. It will go that way with cooking anyhow and it will not change the taste nor the end texture.