Hi Holger,
I ran the Shootout benchmarks[1] which I'd recently updated on cogspurlinuxht 3397 and 3648 using the latest Squeak Trunk image, and the latter performed better in three benchmarks: reverseComplement (-20%), pidigits (-30%) and fasta (-40%). For the rest, the performance of the two VMs were the same.
So, I suspect there's an area not covered by these benchmarks where you experience the slowdown. Or there's some other difference responsible for the slowdown.
Can you tell us more about your benchmark?
Have you tried profiling it?
Levente
[1] http://leves.web.elte.hu/squeak/Shootout-ul.19.mcz