So, if the disks were not ejected between tests, subsequent tests may get an unfair advantage, as the system may cache data that it has already accessed in order to speed up future similar operations, so Photo Mechanic may be benefitting from that. .
That being said, let's consider the data transfer from the card reader to Macintosh HD, where you said 1GB of data took 30 seconds. That is roughly 30MB/sec. USB 2 maximum speed is 60MB/sec (which is rarely actually achieved in practice), while the earliest USB 3 devices were capable of ~600MB/sec, and newer USB 3 hardware can achieve speeds even faster than that. This makes me wonder if the connection with the card reader is dropping down to USB 2 for some reason. Is the card reader's plugged in to a hub of adapter of some kind? Do you have any other cables to test?