This could have been a dummy field on the form.
Card present indicates that both the card and the customer are present at the time of sale, most payment processors also charge lower fees if the card is swiped vs typed in.
That being said, when a card is swiped there is extra information on the magnetic strip that isn't typed in. Payment processors usually receive the raw data from the card, which they then use on their end to execute the transaction.
So either this form input is a dummy, or they're using a card processor that allows them to claim the card was present. If you could post a link to the merchants site, we'd be able to take a closer look at what exactly that checkbox does.
After examination of the site in question, it appears that they are using a payment processor named "Converge Virtual Merchant". Their documentation on processing transactions is available on their site, located here https://www.myvirtualmerchant.com/VirtualMerchant/download/transactionProcessingGuide.pdf
Quickly reading through it, it does state the merchant has the ability to mark the card as present for hand-keyed transactions. The payment site in question is locked to say the card was present.
PCI compliance is for storage and security of cardholder information. Because the payment portal itself is hosted by the processor, it appears that it is indeed PCI compliant.
That doesn't negate fraud though. While your card information is secure, it appears as if the merchant COULD BE attempting to commit fraud by marking all transactions as card present. Since card not present transactions usually have higher fees to account for their risk, the merchant would be defrauding the payment processor by applying the lowest fee and moving that risk onto the processor, in this scenario. However the allegations of fraud and its implications is something that should be discussed on the Legal StackExchange site.