I have also seen this happen with a linked rez. If the primary has not checked in, the sub has not been able to check in. Now that your wife has checked in, try again. No one at AA could see this as being a problem and found it out by trial-and-error. Fortunately, I usually know my travelling companion's PNR and I have been able to check them in and then do mine.

Also, they have reinvoked the no second PB until within 24-hours of second leg. A trick I use is to print the BP to a .pdf file when first checking in and then eMail the file to my Yahoo!Mail account so it's available from the hotel PC if I need to print it later.