Hi PR,
I have the same problem, and even though I did not (yet) fix it, this is my current thinking.
First off, the problem is intermittent---sometimes it happens, sometimes it doesn't. I don't think it's a mechanical issue. What I notice is that when this happens, there is a lot of air in the piston chamber after pulling the shot, which raises the lever if I let it go immediately afterwards (and would cause a little explosion if I were to remove the portafilter immediately, which is not a good idea).
So it seems obvious that the piston chamber draws air when pulling up the piston. That air keeps the water from flowing in, and will only slowly get released after the shot. The air can really only come from two ends [*]---either from the top of the piston past the two rubber piston seals inside, or from the bottom, through the portafilter or past its seal against the group head.
I think the latter is more likely. If the piston seals would let air through, they would let the air go on pushing the piston down [**], but at least in my case the air cushion remains inside until after the shot. I guess it's possible that moistening the rubber improves their seal, which is consistent with the observation that the problem is much more likely to occur on the first shot than on subsequent ones. But for the moment my money is on the PF/group seal, as that is the one that is exposed and thus more likely to be affected by outside influences (e.g. it can get soiled by coffee grounds etc.).
It's amazing how complicated the failure modes of such a simple device can be...
Cheers,
-- j
[*] When first using the machine, or after a break, there is also a small amount of air in the pipe connecting the tank with the group, but assuming that you flush that pipe initially, that should be gone.
[**] There is one effect that occurs rarely, but which I find very confusing: Occasionally, on pushing the lever down, something "bubbles" inside the piston chamber, letting the piston go down a long way without much resistance. It's almost as if water is rushing past the piston seals, althoug I am not sure that that is the case.