Here's a quick check. To do this check, you'll need the program portcheck.exe, which comes with most MegaTune versions, including the one on the DIYAutotune.com website. You'll find it in the MegaTune2.25 folder. If you don't have a copy, download it here:
Power up the Megasquirt and connect it to your PC. You do not need to open the case and should not put the boot jumper in place for this test. Close MegaTune if it's running, and run the portcheck.exe program. When this program starts, it will scan the available COM ports.
If the port it's scanning is not connected to a working Megasquirt, or it's on the wrong speed, it'll say "No connection made." If it's on the right port and right speed, it will give you the version of the Megasquirt firmware that's on the Megasquirt. Note that some Megasquirt firmware versions will look like earlier versions with this test - for example, 029V identifies it as 029Q. This is for backwards compatibility.
If you get a port where it replies with "S" or something else that doesn't look like a firmware version, this port is probably a fake COM port that echos back everything that's typed.
Let me know what results you get. If you could post a screen shot, that would be great.