Hi Walter,
I had the same problem as you when I ported my FPW 2.5 application to VFP 6.0. I solved my problem adjusting my join expressions in order to they match to the ones defined on the indexes. I played a lot with SYS(3054,1) and SYS(3054,11). The end result was almost exact times between both versions. I don't know if Rushmore internals has changed from FPW version to VFP 6.0, but at least for me it seemed to behave differently.