@Nobbir:
I'm currently running Windows XP 32 bits Professional (but will be moving to 7 64 bits soon).
The lines are indeed my target features. I've attached a screendump of my field mapping below.
I realize my feature class names are quite long, but the mapping seems to go right here. However, the result is wrong.
[ATTACH=CONFIG]13336[/ATTACH]
Maybe my long feature class names are abbreviated in such a way that their names become identical somehow, causing the tool to mix up the SHAPE_Length fields?
@Dan:
I already tried Copy Features, but strangely enough, that didn't reset the SHAPE_Length. Only export and (re)import via shapefile did the trick.
I would say that the issues related to the Spatial Join are severe enough (disruptive for workflow, maybe even for data integrity etc.) to issue a little patch until SP5 (or 10.1) comes out.