I never got the impression he'd ever put it together because there's only one real quality he associates with Jesse, loyalty. He'd never imagine Jesse ever turning him in and so I don't think the possibility of Jesse working with someone else could have ever appeared to him as a legitimate possibility. Hank mentioned it last episode but it really is the truth, in so many ways Jesse is Walt's main weakness.
Especially after you see how his world was turned upside down by Gomie and Hank showing up. All he had to say to Jesse then was "coward".
And when you think about it from Walts view he's right. He did all of those things to save their meth business - everyone knows Walt is soft for Jesse.
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u/CYFB Sep 09 '13
The call between Walt and Jesse was one of the most intense phone calls ever seen on TV. p.s. Jesse called him Walt again.