BANG!!
Sorry Chris, I couldn't resist that. I THINK I MAY HAVE A SOLUTION TO YOUR PROBLEM.
We have an iMac DV-SE and bought the Pronto in May of this year. We knew the USB connection was going to be a bit of a pain but didn't realise that it would take this long before cracking the problem of successfully uploading and downloading configurations. We tried Softwindoze 95 using a variety of USB adapters without any success. Now we are running Virtual PC 3.03 with Windoze 98. The problem of the adapter was finally solved when we invested in a Keyspan High Speed USB Serial Adapter which supports data rates up to 230Kbps – twice the speed of the standard PC serial port. At first we couldn’t get it to work, but then I remembered seeing a posting by Cole on this forum back in May. I have reproduced his instructions here, substituting the high speed USB for the twin serial one he used.

Launch Virtual PC. Choose "Preferences" from the Edit menu. Make sure USB is set to "Enabled," but don't select any devices. If there are devices listed don't check them. Select either Com 1 Port or Com 2 Port and click the radio button next to "Mac Serial Port." Under the pop-up menu directly below, you should see "P#XUSA19W" (where "X" is either a 1 or a 2, depending on which USB port on your Mac the Keyspan adapter is connected to). Also check "Non-modem device."

Open the Control Panel folder in Windoze 98. Double-click the "System" icon. Select the "Device Manager" tab at the top of the window. Click on the + sign next to the "Ports (COM & LPT)" item to expand the list. Select (click on once) whichever port you selected in step 3 and click "Properties." Click on the "Port Settings" tab at the top of the window. In the "Bits per second pop-up menu, select 115200. Click OK, then OK again.

Launch ProntoEdit (we are using version 1.05). I have found that it's a good idea to go into setup on the Pronto and extend the "LCD" and "LCD Light" time to about 120 secs – this saves having to keep the Pronto "awake" during upload/download by tapping the screen. Choose "Upload from Pronto" from the File menu in ProntoEdit to verify your connection and sit back in amazement.

I have found this works very well. Contributors to the forum have advised holding down the left and right keys on the Pronto when inserting the cable, but I have found this to be unnecessary. I have also experimented with pushing the cable in both fast and slow. Once or twice it has failed to connect properly the first time, but it usually connects ok the second time.
We bought the Keyspan from www.jigsaw24.com for about £50 and it arrived within 24 hours. Great service. But do make sure you get the High Speed USB adapter, because the ordinary Keyspan USB adapter was not fast enough.

Hope it works for you

Best of luck, Caroline