The reason given of why the Alter Rebbe was chozer on some Psokim later in his life in the Siddur is, because he originally tried to Paskin like the Mogen Avraham as often as possible, as seen in his Psokim in SA HaRav, but later in life he was cholek with several Psokim of the Mogen Avraham, one famous one is by Sof Zman Krias Shma, where in the SA he holds like the MGA, but in the Siddur he was chozer and Paskined like the GRA.
(Shu”t Divrei Nechemia, Shu”t Tzemach Tzedek)
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