Why does my procedure run slowly until I update statistics?
SQL Server uses a cost based formula for determining how to satisfy queries. 

"It'll cost 10 random reads in a billion row table vs 1000 sequential reads. I think I can satisfy the needs faster by doing the 1000 reads since they'll all in order" and decision made off it goes. Unfortunately, when the engine opens the data file to find those 1000 sequential rows, the data has been updated and instead of living in there, there's simply a pointer saying "sorry we had to move, try this address in the next state" And you now have 1000 forwarding rows to contend with. The database engine can't go back and say let's try re-evaluating this costing metric because those 10 reads sound a lot better.

That's probably what is happening (simplified) with your data. The statistics on your data distribution are all out of whack after your ELT processing which is typical-you've just moved a pantsload of data so what was true before may not be as true now. Depending on usage, I will have an explicit call to a reindexing job (thank you Ola) after ETL is complete so that now that all my data is up to date, I need to get all the metadata the server uses up to date as well.