Science! What follows is my bogus hypothesis, with pictures (annotated in the conventional style) and annotations to bolster my unsubstantiated claims.
Other (non-Chemex) cone-style (and basket-style) filters often have ridges down the inside of the cone. It seems that these ridges serve two purposes: to provide channels down which the coffee can flow, and to help "wick" the coffee away from the filter. This seems to help the coffee drain faster. This is probably due to properties of water like cohesion, adhesion, surface tension, and perhaps capillary action (legitimacy of these claims is left as an exercise to the reader).
Contrasting the two types of cones:
between a ceramic cone filter (white, left) and the Chemex cone (glass, right). I think the ridges prevent the "wells" from forming. With a flat surface (like the Chemex), the filter somehow "seals" itself against the side of the cone, restricting the flow of coffee well enough to cause the pooling you describe. I assume this happens because the grounds get packed solidly at the bottom of the cone, and perhaps expand slightly. I don't have a better answer for "why" this seal happens. Lifting the filter (as you describe) breaks the "seal" and permits the coffee to drain.
Another way that I sometimes resolve the issue is to slide a bamboo skewer (or stir-stick, or chop-stick, etc.) between the filter and the Chemex cone (careful not to tear the filter!). This seems to work by providing a similar "ridge" that the other cone filters provide; it prevents the coffee-pockets from forming next to the skewer. I have also tried to fold little "pleats" in the filter, but it's annoying and doesn't work all that well.
I find that this "pooling" happens more often when I use a finer grind. I think a finer grind packs itself down more in the bottom of the cone and clogs up the filter more quickly. Both of these could believably cause the "sealing," but I don't have any other real evidence. It also drains more slowly in other drip brewing methods also. For these reasons I use a coarser grind when using the Chemex than when I'm brewing pour-over with the ridged cone filter. In fact, the Blue Bottle Chemex brewing guide suggests a much coarser grind than regular filter coffee, like that of French press. Maybe that's for the same reason.
The pour-spout on the Chemex helps with this a little by allowing steam/air to escape from the bottom chamber. A pre-wet filter can sometimes slide down into the pour-spout and nearly seal it, which will also make it more difficult for the coffee to drain, but it sounds like that's not what's happening in your particular case.
