This was my response after a few emails back and forth:
I think you have given us some information that is important for us to know!
During the transfer, you simply move the cursor (loop or other tool) into the mouth of the tube and down into the medium. There are popup notices when the tubes are flamed and when the inoculum is picked up and dropped off in the sterile medium. No need to hold down the left or right mouse button during the transfer.
When I tried a transfer in which I clicked the left mouse button when the tool was in the inoculum medium, it did not pick up the inoculum. I then transferred to the sterile medium and clicked the left mouse button and when done, the stoplights were red for inoculation and green for contamination - as if the test had never been performed. You are not imagining things, though I am not sure why you got two green lights - that doesn't seem possible since a successful transfer is what triggers the inoculation light to go from yellow to green.
SO, we'll work on this. In the meantime, DO NOT CLICK the mouse during the transfer and see if this helps! We will try to make that clear to others who use the software and may have experienced the same issue.