Acronis will do it, I have a flash drive with two partitions as we speak that I created using Acronis.
The problem is getting Windows to recogonize the second partition, which isn't easy, as I'm sure you found out via google. The second partition is there, created by Acronis, but Windows doesn't use it or assign it a drive letter because most flash drives are marked as removable and Windows will not allow removable media to have more than one partition, and if you create a second partition with a 3rd party utility such as Acronis, Windows will not recognize it.
So you need to find and use one of the many work arounds out there to make Windows detect the drive as a fixed disk, and not removable.
The problem is that most of the work arounds change Windows, and not the flash drive itself, so it will only work on the single Windows install you apply it to. If you move the flash drive to another computer, the second partition will not be seen...
The only real way to change this is to change the Removable Media Bit. Changing the Removable Media Bit will allow both partitions to work on all Windows systems. BootIt does this on some drives, but not all. I don't know of a tool that works with all drives. I know the Removable Media Bit is in the SCSI Inquiry Data string, but I don't know how to change that on a flash drive.