Removing batteries would not have an effect on your FICM tune. Your truck is probably going through a relearning cycle to adapt to you and your driving. When the batteries are disconnected the "RAM" is lossed and the computer has a bit of a learning curve to go through.
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-Nick
2005 F250 Lariat; CC LB; 6.0 PSD; Edge CTS w/ PHP custom tunes; EGR Delete; ARP Studs; 4" Turbo Back (no Kitty) w/ 4" straight thru muffler; Rev-X; FICM programmer
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