Sometimes the WUs are 'larger' meaning that they have more steps or frames, but are worth less (fewer points) usually because they take less time to complete the entire WU. I've had some that take 23 minutes per frame, and some that take 8 seconds per frame. The one I'm working on has 250 frames, and will take about a day to complete. One other computer is munching away on a WU with out 30000 frames. I don't know the points they're worth, I'm obsessed enough just with the processing time of the different WUs, I'd go crazy analying the points (average points per frame/points per hour, etc, etc, etc)
Proteins, they're a weird thing. Some are much more complex than others. Hence, some of the WUs are more complex than others, take more of your CPU cycles to process, so they reward you with more points...
Here's something I've noticed and maybe someone else can confirm it:
I can gain the most points by configuring F@H to fold deadliness WU in batches. In other words, if I let F@H download WUs with deadlines one at a time (the default behavior), then I will get less points.
FYI, I allow large WUs in both cases (I don't think that should matter though).
Has anyone else seen this?