I can pretty much dupe this at will (I've deleted and created new paycheck via the Wizard several times).
I go to the Calendar, and find the upcoming paycheck and edit it (you double-click on the calendar date and it'll pull up a list of everything scheduled for that date). Select the desired item and edit it. This should edit "this and all future instances". But it does not.
In this case, the paycheck wizard (this may be where the original source of the bug is at), gets deposited in to a Checking account. Some of the pre-tax items like 401(k) contributions should be transferred to the 401(k) account, but instead, Quicken saves them as being transferred to the same checking account, thus the amounts never get into the 401(k). Even when I edit it, change it, and save it, I can go right back in and voila- it's back to the Checking account.
Now, if I Enter the paycheck (click Enter) and edit the account (have to change from checking to the 401(k) account for the line item in question), and then save it, it'll process that check correctly that one time. [Edited-Readability] But kinda defeats the purpose of doing this via a paycheck wizard.