There are serious problems with ALL FOUR of the flights in question, including Flight 93 being BOARDED TWICE in Newark.... the result of an unplanned snafu.... it's all in the link below.
This chart taken from:
http://www.bts.gov/xml/ontimesummarystatistics/src/dstat/OntimeSummaryDepatures.xml
BTS - Bureau of Traffic Statistics showing Flight 11 never departed from Boston Logan international Airport on 9/11/2001.