(They recommend 25Mhz) Did you provide that? I suspect they did not include a crystal in the LEPTON to keep the size down and embedded devices usually have access to some kind of constant clock any way. Now we know Raspbian is not very great at generating consistent clock rates consistently so you may be experiencing problems with this - The same way may other FLIR'ers are experiencing. I assume you got it hooked up to SPI correctly but one of the problems seems to be the Input Clock rate.
So looking around really I noticed the protocol used on the Lepton is VoSPI (Video over SPI) Frankly never heard of that before but its plausible because the frame size is 80 x 60, which is not a crazy amount of data with some kind of AGC applied format which is selectable (Did you select the correct one?)
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