Yen vs. Swiss Franc
Currency movements often happen without any shift in fundamentals, so there might any explanation in that sense (although there are always some form of cash flow explanation), but in this case there are actually two good reasons why the Swiss franc has performed worse than the yen.
One is that Swiss banks have made a lot larger losses on the American mortgage market than Japanese banks. In the last few quarters, we have seen a significant decline in Switzerland's large current account surplus, despite a rising trade surplus. The reason is that the previously very large investment income surplus has been wiped out, which the statistics authorities point out is due to "turmoil in the financial markets resulted in losses in the bank's foreign subsidiaries". The decline is in the order of CHF 13 billion in just one quarter, which is equivalent to 10% of GDP.
The other reason is that the Swiss franc has been dragged down by the decline in the euro. As Switzerland is completely surrounded by the euro area (except for Liechtenstein, but that country is so small that it really doesn't count), most of its trade is with these countries, and so its currency is affected by the movements of the euro. By contrast, Japan has a far smaller dependence of the euro area as foreign trade is a much smaller part of its economy and as most of its trade is with other parts of the world, primarily the rest of Asia and the U.S.