We don't know how much time passed between signing the Deal of a Lifetime and Stanley conquering FAQ, so that's up in the air. And I still think it's plausible. Jack knows Jillian really, really well, and has an incredibly deep understanding of how the mind works. He knows that Charlie and Betsy went into her head to fiddle around with things. He's an Eyemancer, so he has to have some inkling of what could be done to her in there. And thereafter, Jillian starts acting differently.
Jack's a smart guy, and with the way his mind works and his love of riddles and teasing at meanings, he'd catch on quickly. And he cares about Jillian, knows about her ordeal with the Buds, and would be watching her closely. And he knows about the Deal and would be aware that Charlie was going into her head. And when you add it all up... if there's any unit in all of Erfworld who could possibly figure out what was done to Jillian, you have to admit - it's Jack.
The difficulty I imagine Jack would have in discerning the change in Jillian is doing more than chocking it up to her relationship with Wanda.
Three main things changed for Jillian at the beginning of the Deal of a Lifetime:
1. She was hooked on, then cured of, heroin bud addiction.
2. Her head was made a playground for Charlie/Betsy
3. She fell in love with, and spent most of her leave time with, Wanda the new FAQ croakamancer. In a Dominant/Submissive relationship, no less.
Yeah, it's possible he could have spotted #2, but discerning personality changes due to #2 from changes to to #1 and #3, without knowing #2 even happened from the start, and without getting to spend all that much time with Jillian?
That's asking a lot, even from Jack.