It's been a long time since I last used Cygwin, but since it's "just" a compatibility/emulation layer, I wouldn't be surprised at all if there were issues with its handling of serial ports and/or the interaction of Windows, Cygwin and Device::SerialPort. Have you tried accessing the serial port from inside the Cygwin environment, for example via screen? Also, and this is a complete stab in the dark, perhaps the baud rate setting is getting messed up somehow, and you could try setting the default baud rate of the port in the Windows Control Panel in the Device Manager.

If you're not entirely fixed on Cygwin, as a possible alternative, Win32::SerialPort should work under Strawberry Perl (I have seen at least one report that someone had to use the 32-bit edition of Strawberry Perl even on a 64-bit Windows, though).

You asked about other alternatives: Yes, there are some more "low-level" ways of opening and communicating with the serial port in Perl, but in my experience those can sometimes become so tricky to get right that it's probably better to first try to get Win32::SerialPort or Device::SerialPort working.