Hi,
Thank you very much for your detailed ticket. I was able to replicate this setup and found the cause. Generally it is not a common practice to use multiple instances of the same custom field by name to store multiple values, but WordPress allows that, so it should be fine.
The problem with this is, that the plugin query applies this logic one a single field level – so the value1 AND value2 means, that it should match a single existing field value, not one value in one field, and another one in another field etc..
I was able to come up with a possible solution, but I will have to extensively test it before a final release. We have a minor bugfix release planned for this week, a solution to this should be in it as well (by adding a new logic option).
You will get a notification from codecanyon once the update is ready, should take a few days, if that is okay for you.