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You should be fine then. Your wife will not be out of status after 5/5/01. Since you are in the AOS stage, there is nothing like a "OUT of STATUS" issue here. The advanced parole is valid for a year. May be that is the reason that the Immigration officer stamped the passport as mentioned.
However ever, if your wife wants to travel abroad again, you might want to consult your attorney. When you return back during the AOS stage, you should have a valid AP document from the INS. I am not sure if the stamping on I-94 will stand as against the actual parole document from the INS.
Any thoughts from the board guys......
TIA