Ask around and there will be many theories proffered by different road users to explain the great CTE congestion.
One popular theory (especially among my biker friends) is that the jams are caused by CTE's numerous inclines. And Singaporean drivers, being frugal with their fuel, do not accelerate more upon coming to an upslope. What happens is a "wave effect"; where you see a clustering of vehicles slowing down on the upslope and a gradual spacing out of cars on the downslope. This slowing down effect is compounded over the number of vehicles and hills such that eventually, some drivers have to tap on their brakes to avoid rear ending the car in front. This further compounds the effect and eventually creates jams when there are sufficient number of vehicles.
A slightly less complicated theory derives from the fact that CTE serves a particularly populous part of Singapore - Ang Mo Kio. Add the fact that the population density is high (substantial HDB estates as opposed to landed housing) and tends to be doing decently well (HDB prices are generally higher in Ang Mo Kio) and you have a huge pool of car owners who need to use the CTE. The sheer numbers of drivers cause the congestion.
The final theory I have come across attributes the congestion on CTE to its expressway design. Advocates of this theory will point out that in certain stretches of the CTE where jams are the worst, there are just too many entrances and exits in quick succession. As vehicles switch lanes to exit or enter the expressway, they have to brake or will cause others to brake or slow down. This disturbs the smooth flow of traffic and causes congestion. This is compounded by the fact that there are quite a few entrances or exits that coincide on the expressway - meaning that vehicles enter onto the expressway in a lane shared by those trying to exit the expressway. This makes entering or exiting the expressway more difficult and aggravates the disruption effect of vehicles entering or exiting the expressway.
My personal take is that I favour the last theory. This is based on my personal observations of how traffic flows on the CTE as well as the fact that AYE is also the most congested at the stretch where there are 3 exits in quick succession (Clementi Ave 6, Ave 2 & Clementi Road).
What is your theory on the CTE jam?