UD is well aware of the problem of long running molecules, hopefully there will be a solution allowing for user determined saves soon. It's unfortunate that there are cases where you lose processing time. It happens to me whenever Win95 crashes, which is expected.
In terms of the percentages, you cannot attribute it directly to time. The percentages seemed to be based on the number of molecules that need to be examined, and the number of conformers for that particular molecule. Some work units are more complex than others, and will take more time to complete.
If you crash or reboot you will lose the results for molecules since your last save. You can use UD Monitor to help track when your last save was.
In terms of "throwing out" molecules. I personally don't see the difference if I'm running SOD, TK or RAS. Each one can be either short or long. Regardless of the time it takes to process a molecule, the points I would generate over a specific time frame are the same, regardless of how many work units are processed. Besides, I'm not in it for points/prizes (other than reaching a new avatar level here). It's more important to be making a contribution that might just make a difference one day.
If you are running the agent, and it has been a Loooooooong time since the last save...suck it up, and let the molecule finish. Ctrl-Alt-Del'ing your computer and deleting the workunit accomplishes little. Let the little bugger finish on its own.
-Tacks
