On 11/28 I rode from Strasbourg(France) to Basel(Switzerland) by train. Between Mulhouse(last stop in France before Basel) a Swiss "official" came through the train inspecting passports (he could have been customs.) The train proceeded into Basel SNCF and then departed and arrived in Basel SBB--at this point you are in Switzerland, so there would be no more passport checks. The advantage (even with the delay of getting from SNCF to SBB) is that connecting trains (to other points in Switz.) are much closer.
This was true on 28 November 2008 when you travelled, but since the middle of December 2008, Switzerland is part of Schengen, so there will be no more passport control. There might still be custom officers checking whether you are smuggling goods! Although when I was at Waldshut station (on the Swiss/German border) a few weeks ago, the way to declare goods was to post a letter in a mailbox. Not sure this really deters smugglers!
I then took a regional train from Waldshut (Germany) to Friedrichshafen (Germany) and interestingly, it passes through Schaffhausen (Switzerland) and even stops there. I am wondering whether Swiss customs officials could have boarded the train? Or was the relevant platform at Schaffhausen a kind of German customs area?