boot - Problems formatting USB stick to be bootable (with PeToUSB and Linux)

I'm trying to make a USB stick installation disk for Windows XP. I've done this several times before (using this method), but now it's failing, and I don't know why.

The only thing that's going wrong now is formatting the USB stick, which is PeToUSB's job.

One of my USB sticks is recognized, but it's bigger than 4GB, and PeToUSB fails to format it with FAT 16.

The other is smaller than 4GB, but it's not being recognized as a USB stick by PeToUSB, nor by Windows (I tried on XP and 7), both see it as a fixed hard drive.

I already tried to zero-fill, re-partition and re-format it, but the problem always keep happening.

Then I tried formatted it using fdisk + mkfs.vfat on Linux, and with Gparted, always using FAT16 and setting LBA flag on, as PeToUSB would do, and then skipping to the next steps.

But it never works, it just doesn't boot. Formatting with fdisk + mkfs.vfat it doesn't do anything (Even though it have the 0xAA55h code on the last bytes of the boot sector), and when formatted with Gparted, it gives me a message that the disk is not bootable (this message is displayed by the code on the USB stick, and not by the BIOS).

So, my questions is:

Does anyone know how can I format it as PeToUSB does, or know how can I format it properly?

Thanks!