I suspect the partitioning method is the key difference.
Two details:
- does your version of linaro-image-tools use gparted or sfdisk? 
- does your version of linaro-image-tools 'dd' the partition table
(e.g. the first megabyte) clean before calling any partitioning agent?

I'm using the version of this package directly from source control and
I've not noticed any problems but I'd be interested to know of any.

I've tried partitioning every which way with a variety of tools and tried both letting linaro-image-tools overwrite the partition and leaving it alone.

I don't think it's a problem at all with the linaro-image-tools.