The rule looks like it is saying if there are any items in the cart, and the checkout country is US and the total is >= 100 and the fax variable is set to 1, then shipping is free.
The next shipping rule that you have though looks like it says if there are items in the cart and the fax variable is set to 1 and the order is less than 100 charge 9.95.
It does not seem that these rules are conflicting with each other. Just to clarify you would like to charge 9.95 for shipping when the fax variable is set to 1, unless the amount is over 100 and the checkout country is US, then free shipping correct.
Please post back with a copy of your WA_eCart folder from your site and I will do some testing to see what may be going on.