You should try redownloading the bot and starting from a fresh copy. I just re-tested it on the latest Beta and it looted them fine.
Match Any sounds a little confusing, but it's basically changes how the evaluator matches names or types.
When it's enabled (checked) or indeterminate (square), an item will match that filter category if its name or type is found in the list of names or types the user specifies.
When it's disabled (unchecked), an item will match that filter category if its name or type is not found in the list of names or types the user specifies.
So for example, if you wanted to pickup all currency, except for a few items, rather than making a filter for each item you want to pickup, you can use the general currency rarity along with a disabled Match Any setting for names and list the currency names you don't want to pickup. That is what the "Pickup all currency except..." filter does, if you check the default filter generated. Likewise, with Skill Gems, you can exclude some by disabling Match Any, which is also shown in the default filter.