OK, this is just absolutely fascinating! (and I found my thesis)

The tale of the Alcmaeonidae treacherously signaling to the Persians with a shield is, to me, quite extraordinary, and I cannot accept it. -Her 6.121

I do not think Herodotus is saying this is untrue. I think he just finds it unbelievably shocking that his fellow Greeks actually wanted to help the Persians. Some historians say these signalers were Persians not Athenians. But I don’t agree. There is plenty of evidence of Greek treachery, including and especially some Athenians who were pro-Persian. (it was because of treason that Persia was able to easily massacre the Eretrians)

The Persians were friends of the tyrant, so it is not too far fetched to say that tyrant families in Athens were trying to gain back control or felt that helping the Persians take Athens would be beneficial to them.Some also say the signal was some type of code to direct the Persians. But the distance (over 5 miles) makes that unlikely. I think the only thing this sugnal said was to tell Datis that the Athenian citizens are not revolting. That’s why after seeing it, Datis immediately turned his ships around and went back to Persia. The signal could also mean that the Athenian army had returned to Athens. One of Datis’ strategies landing at Marathon was to draw the hoplites away from Athens. I don’t think he expected them to have returned to Athens so quickly.

More information

For a good view, if you have access to JSTOR (like AMU finally does!! WOO!!) check out “The Shield Signal at the Battle of Marathon” by P.K. Baillie Reynolds. Journal of Hellenic Studies, vol 49, Part 1 (1929). The author shows the various arguments and is of great assistance in helping me rip apart the historians who say they were Persians.