I'm too busy with other things right now and I don't have an empty memory card available, but aefdisk32 can at least dump the partition table of my SDHC card, so I guess it can also partition it. I have no prior experience with the program but I'm sure someone can figure it out from the following basic instructions:
1) Find SD card drive number (aefdisk32 X /show, replacing X by 1, 2, ..... until you find your card)
2) Trash SD card partition table
3) Create 16/32 MB FAT16 partition
4) Format it, put CHDK on it and make it bootable (card tricks?)
5) Create [remaining size] MB FAT32 partition
6) Change partition type of partition 1 to 0
and you should be all set. These steps should not require the special driver, so please test without it installed. I hope this method works 
Thanks DataGhost for the instruction and the hints of the process. I spent three evenings trying to figure out how to make my new 8GB card work with CHDK and S5IS. First I tried the method described on
this page, but unfortunately it didn't work. Then I tried to play with aefdisk32, but the problem is that when you change the partition type to 0x0 aefdisk32 wipes out the whole partition data instead of just changing the type. Saving the data to a file, changing it and then restoring didn't work with aefdisk32 either - the restore function apparently doesn't work properly. Hence I spent some time finding an app which will just change the partition type and I ended up with Beeblebrox NT. And then everything was finally in place. Below is a simple instruction:
0. Get all of the software needed for the setup.
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aefdisk32.exe - to create partitions
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Beeblebrox NT - to change partition type
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bootable.exe - to make card bootable
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CHDK firmware - actual CHDK
1. Unzip all downloads, install Beeblebrox.
2. Start CMD.EXE in the folder where the programs were unzipped.
3. Find SD card drive number (aefdisk32 X /show, replacing X by 1, 2, ..... until you find your card). In my case the number was 5.
4. Create new partitions. Example: aefdisk32 5 /delall /pri:16:6 /pri:0:c /activate:1. This command deletes all current partitions from the card, creates first 16MB FAT16 partition and whatever is left on the card as FAT32 partition, activates partition 1.
5. Find the drive letter assigned to the first partition and format it. (You can use either command line format or do it through Disk Management GIU). In my case the letter was I: for the drive.
6. Make your drive bootable using bootable.exe. Example: bootable.exe i:.
6. Copy DISKBOOT.BIN to your drive.
7. Close CMD and Disk Management. Run Beeblebrox NT. Choose your drive from the drop-down. Since Beeblebrox NT starts numbering from 0 the number of your drive should be the one you found with aefdisk32 minus 1, which is 4 in my case. Change the type of the first partition on this drive to 00 and save the changes. Then close Beeblebrox NT.
8. Windows now will see your second partition and show the first as unallocated space. Format second partition.
9. Take the card out of the reader and lock it.
10. Enjoy your CHDK on a FAT32 formatted card!
In the future if you need to change CHDK you will have to run Beeblebrox NT again and change the type of the first partition back to 6, make all the changes and then change it again to 0.
Hope this instruction helps.