From ~May, 15 Reddit is cracking down on account farms

they have been getting tougher for a while now.honestly how are you handling 1000 accounts manually?there must be some sort of automation that is taking place which can be a reason why these accounts are getting shadowbanned.

From my knowledge you must have the PERFECT setup and you should be cautious on behavior patterns (this is not something I yet faced but everybody says it and I agree). An account which starts from X hour and finishes to Y hour EVERYDAY will sure be flagged. One more note is that maybe one account from your whole network, if it has bad setup, might flag your whole network. Also, I'm not sure on what you use those accounts, but be aware of some banned/flagged keywords (such as black hat niches)