This is a complex problem that is not due to problems inherent to PS. I suspect you are trying to do too much with too little in terms of computer horsepower.
Without buying new hardware you can make sure that all background programs (like virus and firewall) are shut off and unneeded background processes are shut down in task manager/processes. No matter how much RAM you have Windows has finite software "resources" for tracking everything the computer is supposed to be simultaneously doing.
If you have a separate swap file hard drive, and you need one for files of this size, make sure it is set up properly and has enough contiguous space (defragment if necessary). This is your virtual memory. Although Windows will tell you some enormous amount of virtual memory is available, basically the entire hard drive, Windows will run out of software resources for complex processes long before it can use all that virtual memory. If you can have another hard drive for a PS scratch file performance may improve. You can watch what is happening by bringing up the Windows Task Manager and watching what is maxing out in the performance tab.
When you run your processor and RAM hard, as happens when they are trying to process this much data, your system might overheat and cause a crash. Take the side panel off your box and see if that helps.
If you can double your RAM your problems may improve; there is no real point going above 2 gbs RAM.
Any computer can stumble/choke running multiple D2x full size 16 bit files through the HDR process. This is one of the few things you can do with your computer that makes it breathe hard.
If you can reduce the file size prior to beginning the HDR process you may be able to avoid crashes.
If you really want to process this much data routinely you need to consider a new computer with a dual core processor and at least two hard drives. I have a dual core Athlon with 2gbs of RAM and 3 hard drives (they do not need to have giant capacities) and while it takes a while, at most a couple of minutes, I have had no trouble running 5 full size D80 files through the HDR processor in CS3.
I called tech support on this one. I got it to work by rebooting in selective start up with no processes running but what was need to PS. Time for a more powerful machine. And yes, you do get full tech support right after your purchase.