Did you try pressing vol +/- keys together same time when in stock recovery? Then choose to wipe from menu. See if that works?
If you can connect boot loader then PC should see it... maybe it takes awhile to load all the drivers.
When I had to reflash ('cos I bootlooped it) I connected in boot loader, waited for PC to recognize everything, but phone wasn't showing in list. Provided that the PC did make that usb connected sound then just press flash anyways, it may take a few minutes to start working though.
What file are you flashing with? It helps to have .sbf that can actually go in your phone.