Interesting. So I took a tournament and exported from version 3.1.1 and version 3.3, and then compared the exported files. They files were identical except for the very first line. In that first line is an attribute "ShowBuyinByPlayer". For version 3.1.1 I see:
ShowBuyinByPlayer="-1"
For version 3.3 I see:
ShowBuyinByPlayer="1"
Tiny difference, but I looked more closely and saw that the specification showed that the value should be either 0 or 1 (for true or false). Convention is usually that 0 indicates false and any other value indicates true, but not everything is coded to follow that convention. In version 3.1.1, I was setting the value to either true or false, and when the MS XML engine translated it to XML, it became 0 for false and -1 for true. In version 3.2, apparently I changed this behavior to make sure it exported as 0 for false or 1 for true, but I can't find any notes as to why I did it or what prompted it.
I can't say what, if any, effect this may have. But it's possible it could explain what you're seeing, CruiseLite. Looking at the code, I see this is also [still] true for the AllowAddons, AllowRebuys, and BountiesAllowedattributes. So, it could also explain what you're seeing mcfrojd. But I can't say for certain.
You could test this by taking a tournament, exporting it, and then editing the exported XML file before submitting it to StatsGenie. Look for the appropriate attributes (ShowBuyinByPlayer, AllowAddons, AllowRebuys, and/or BountiesAllowed) and make sure their value is 0 or 1 (and not -1), and then submit the file to StatsGenie and see if it makes a difference.