Hi,
I've been able to reproduce the problem with test cases not being deleted properly, but everything else seems to save correctly. I tested the project you sent, and aside from not having the soapUI Project used in the soapUI Runner, the components looked like they were working as they should. Can you try uninstalling and re-installing loadUI Pro? You shouldn't have to touch the .loadui directory, so you shouldn't have to re-activate the license or anything, it should just work. Make sure that the installation directory in Program Files is completely gone before re-installing though.
Regarding the saving issue, this will be fixed in the next available nightly build for loadUI 2.0.x.
Regards,
Dain
SmartBear Software