It doesn't matter how big they are. What matters is whether they extend more than 4GB in to the drive. You said you are using 0.5GB FFS and 2*3.5GB SFS. That means you're using 7.5GB of the drive. If you haven't taken steps to ensure your scsi.device is able to write beyond the first 4GB of the drive then when it needs to do so, it will start writing to the beginning of the drive instead. That overwrites the partition table, hence the disappearing partitions.
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moto