I was able to get into the code on the page and add in some looping for the unitdisplay recordset that you are comparing to. What I noticed for at least the first column of checkboxes was that there is only a single entry for that ref ID. I was trying to test with others that might have more than one value but could not find any to test for this. I checked on all of the id values that I saw in the amenitiesunit table and it seemed that there was only a single Unit Amenity for each one.
This tells me that there might be a problem with your recordsets that you are using for the display, it seems that it only ever has a single record, at least for the unit amenities. I'm including a copy of the page that I updated for your. You will see around lines 286 I added the loop for the display recordset.
You can replicate this for the other two columns of checkboxes by copying the code and updating the reference to the recordset. Please check this out and do some testing with your data to see if the recordset is not working correctly or if there is only a single match for the ones we are testing with.