A few comments in response to all this.

First, for a train to be officially "late" according to the Swiss train companies, it must be at least 2 minutes late. When they publish statistics about the percentage of trains that are late, they use this definition, and they normally also give the percentage of trains that arrive more than 5 minutes late. Comparing it to other countries is difficult because different train companies have different definitions of how late a train needs to be to be considered officially 'late'.

Second, the Lausanne-Geneva line is running at absolutely maximum capacity during rush hours, making delays more likely there than anywhere else. This has been an issue for some years now. There has been a lot of discussion during this time about adding a third track for the length of this route, but the last I heard was that there is still no plan to actually do so.

Third, the LEB is nothing like the SBB, it is barely more than a tram, so should not be considered in the same context. It should only be discussed in the context of the local Lausanne transport system (Transit Lausanne) and not with the national train network (which it isn't even directly connected to).

EDIT: I found an interesting article comparing the Lausanne-Geneva line to the rest of the Swiss rail network, and giving some other useful info. The link popped up in Google, but then didn't work. The cached Google file is here, which hopefully you will all be able to read. Here are some highlights:

"CFF spokesman Jean-Philippe Schmidt said about 94 to 96.5 percent of trains on the line between Geneva and Lausanne arrived less than five minutes late in 2007, compared to 92.4 percent between Berne and Zurich, and an average about 94 to 95 percent nationally. ... “We’re at close to maximum capacity, more than usual in Europe.” With a train every 12 minutes on average nationwide, it’s world record. ... Between Lausanne and Geneva, it needs at least part of the long-delayed third track on the line in order to keep up with an expected growth in demand. Last week [article published in May 2008], senior officials from the cantons of Geneva and Vaud said they were looking at ways of financing it together at regional level for the first time, instead of relying on the usual federal funding. “Around Zurich, regional authorities introduced a policy of financing local rail services 20 to 30 years ago. Western Switzerland’s interest in that has come much later,” Schmidt said."