nkdy
I was thinking about your issues the other night.
The UNO and Duemilanove present themselves as different Com Ports.
I presume you have checked the Com Port settings to ensure they are set appropriately (ie baud, Parity, Bits, Stop bit).
It is possible the two are different, but will not be affected by uploads, since these are overwritten by other parts of the upload process.
The other option may be to monitor the rx/tx pins using another communications program.
In theory it should show exactly what you send in, or what the 328 sends out.
This will be at TTL level, so you may need to convert it, using a suitable level converter (max232, etc)
the ATmega8u2 should be capable of converting incoming and outgoing data at whatever speed it gets it at, so the only thing affecting data flow is the machines com port settings, and the sketch loaded into the 328.
Windows seems to consider the UNO as a modem, as it uses the mdmcfg.inf file when it installs the UNO drivers, while the FTDI supplies a lot more information to windows.
It is possible to reflash the ATmega8u2 using Atmel's flip program http://www.atmel.com/dyn/products/tools_card.asp?tool_id=3886 if you are in any doubt about it.
Good luck with your program.
Mark