In my opinion, since the on-access scanner is "on-access" if you browsed to that part of the file system, it should pick it up.
That's only because the file was transferred from another system on the network. If you used that machine to download the file in the first place, then the on-access scanner would scan it once downloaded (or as it was downloaded).
I don't see it not finding the virus a "huge deal" because I doubt that the virus could do any harm by merely being transferred to another computer. Something has to invoke it, and with that, it can do no harm. It's just another file. Now, when the file is executed, the on-access scanner will scan it as it is loaded, and the virus should be detected.
Or, maybe I'm wrong...