Those would be the secondary windings (referring to OP's first post), not the primary. The primary is where your 120VAC connects.
If all the secondary voltages are half, it definitely sounds like the transformer is jumpered for 220v on the primary. When set for 220V, the transformer has to half the primary voltage of 220 to 110 before reducing the voltages to the required secondary voltages (not really, it's all about winding ratios, but easiest to explain that way). If you are getting half of what you expect, then the transformer is halving your 110.
Unfortunately all the sys80b manuals are locked down by Steve Young so I can't quickly look at the jumper diagram.
EDIT: Pdman beat me to it