LTC mining was 86% more profitable than BTC mining as recently as yesterday.
?! How did you compute that? My computations show that LTC was ~97% as profitable as BTC and is now ~94% for 5870/5970 GPUs. They use a 1/1000 ratio for the hash speed between LTC and BTC. Maybe some progress has been made with scrypt on OpenCL, did it go above 400kH/s on 5870s ? I'm not involving exchange fees and additional power requirements from the GPU RAM not being massively underclocked so my computations are biased towards LTC.
Edit: did the LTC difficulty change recently too? That could explain it (I don't track it and just update values in a Calc sheet when I feel like it).
Even when it did briefly go above 100% in the past, I didn't bother reconfiguring rigs as simply tuning them for the right setting would require hours of work.
Just as some people may be BTC mining at a loss this very second some LTC miners may be mining at a loss expecting LTC prices to rise again.
What isn't clear about buying things at its face value when it's expected to go up instead of buying it at a loss that so many people mine at a loss?