I'm running Windows XP SP2 on an AMD Sempron 3200+
Everytime I shut down the computer and boot again it resumes a big chunk of progress back in time. i.e. from 74% back to 30% or something.
I don't want to let my computer run day and night and usually it can't complete a task during one session.
I've had this problem both with SETI & Rosetta.
With SETI the tasks are so big that I had to abandon as it will never submit since it jumps back too much. With Rosetta if I let the computer run more than 5 hours it could complete but I don't always use it for so long.
Oh and I DO suspend the task and exit BOINC before I shutdown but it doesn't help.

A quick solution would be to Hibernate the system instead shutting it down until a task completes its run. (This is also the only viable solution for some tasks (yes, there are also tasks, which run hundreds of hours between checkpoints), but fortunately there are very few projects with such applications.)

A proper solution would be to also find out, why are the progress jumpbacks that far... What is the checkpointing period for your task? Look for "Tasks checkpoint to disk at most every ... seconds" in your preferences. You can also check running task's properties in BOINC Manager - lines with "CPU time" and "CPU time at last checkpoint".

Peter