I've got an Uno connected via USB. It shows up as COM3.
The Arduino IDE (version 22) is perfectly happy talking to it. If I close the Arduino IDE and open HyperTerminal that also works without any problem.
I've programmed the Arduino to emulate a Weeder Tech http://www.weedtech.com
thermocouple board, but Weeder Tech's software (ModCom) refuses to connect to COM3. I don't think it's a problem with my code, because the error I get from ModCom is "COM3 can not be openned" which happens before any attempts are made to talk to any devices. On a PC with a physical, non-USB COM1 I can select COM1 even though no Weeder Tech boards are connected to it. Also, I can select a serial port from a USB-Serial converter. Just not the Arduino port.
I've tried several different PCs: laptop and desktop, XP, Vista, and Win7. Same thing on all of them. I've also tried manually forcing the Arduino to COM1 on a laptop with no physical COM1 but that didn't change any symptoms. Again, if I use HyperTerminal or the Arduino IDE Serial Monitor I can talk to the board and it responds as I expect it to. It's just the ModCom software that won't see the port.
It seems pretty clear that the problem is with ModCom, but I'm asking here in case anybody else has seen this and maybe has a fix? I'm also contacting Weeder Tech, but I suspect they'll tell me it's not their problem because it's not their hardware.