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Either the kernel, or rather the C compiler and library in 5.2 very slow. I do numerical calculations and when I upgraded from 5.0 to 5.2 the speed of my calculation substationally slowed down (about on third). When went back I have gained the speed back. I noticed, that on alpha from 5.1 the new, and unfortunately experimental compiler, the egcs is used. Since I am not an expertise in kernel compiling, I am not sure where the problen came from. It is because the 5.1 and 5.2 kernel was compiled with egcs or simply the egcs does not give the same speed as the gcc compiler. I think this is a serious problem, since many pepole, like myself, use the alpha station for numerical speed.
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I used the GROMACS molecular dynamics package when I fund this speed problem. I have repeated the install 5.2 and do GROMACS, install 5.0 from scratch compile GROMACS and run severeal times and the major speed problems comes out consistently. As I said the speed problem only comes when one dealing with NUMERICAL (floating point) calculations.