actually i think it's not a problem with version numbering, I think woocommerce needs to upgrade some of it's jQuery and jQuery UI core plugins to be more compatible the new version of jQuery and jQuery UI in WP 3.6.
I had some conflicts in my own hand written jq codes too which where resolved just by removing some depricated codes I wrote for jq 1.8
I don't think the world is quite ready for jQuery 1.10 yet, the very own site of jquery.com is still using version 1.8 and that's ironic.
WordPress guys could have held up more before upgrading the core jq so soon.
That's my guess any how, maybe there's something I am doing wrong.