When a new block is found, mining pools send miners a block template with no transactions so they can begin doing useful work as soon as possible. The pool will then send a block template full of transactions right afterward, and the miners will usually have it in under a second.
Miners sometimes get lucky and find the empty block in the interim period before having the full template however this is rarely the reason for an empty block as it's such a small amount of time.
The usual cause is that some mining hardware will continue to work on old work for up to 60 seconds despite having newer work.
+When a new block is found, mining pools send miners a block template with no transactions so they can begin doing useful work as soon as possible. The pool will then send a block template full of transactions right afterward, and the miners will usually have it in under a second.
Miners sometimes get lucky and find the empty block in the interim period before having the full template however the reason is often that some hardware continues working on older templates after receiving updates.
Contrary to common belief, sending clean=true to the miner does not necessarily mean that they stop doing old jobs, just that they discard the work once completed. In the case of empty blocks this would just result in the miner throwing away a valid block that not only would have rewarded the miner, but added PoW to the Bitcoin's blockchain.