AH! Thanks. The mention of the logging jogged my memory.
I had the same problem. I added logging to *ALL* the related system and User level scripts to try to track down the problem.
*If* I recall correctly the main impact was slowing down things like logging in a little, and multiply "stuffing" my PATH variable because I concatenated the default OS provided PATH value with my own values. I had several directories for a variety of tools that I was using. Altogether in all the directories, there were *MANY* files. Because the startup scripts were being executed multiple times, my PATH variable would have at least two copies of the list of directories I intended to be in it. So if something was searching the PATH for a command that it ultimately wasn't going to find, it took a VERY long to discover that it wasn't there.
I believe there is an environment variable, I'm tempted to say it is something like "PROFILEREAD", that was supposed to prevent that.
Even if it's just an annoyance, it shouldn't happen, because the order of invocation of profile/login/etc. scripts, is documented in the man pages for some of the shells, especially bash.
Unfortunately, since a lot of people are using much more current suse releases like 11.x, I believe the 9.* versions have sort of fallen off the radar for checking bugs. But I'll check...bug # 167306 in Novell's Bugzilla makes mention of the problem, so it is a known issue that was ostensibly fixed.
I think I did some brute force solution like set my own environment variable that the existing scripts in /etc don't about, and so don't manipulate. I then checked for the presence and value of that variable to prevent multiply executing the scripts.
Hope this helps.