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I believe you have to load it as a Kernel in the "boot.ini" file.
Open "boot.ini" w/ Notepad.exe, copy the line under [operating systems], mine looks like this, "multi(0)disk(0)rdisk(0)partition(3)\WINDOWS="Wind ows XP Pro" /fastdetect", yours will probably be a little different. Paste is under the one that's currently there and add "kernel=pathtocygwin.dll" Change the part after the "=" to someting unique, like "Windows XP Pro X"
In the end it should look something like . . .
[boot loader]
timeout=10
default=multi(0)disk(0)rdisk(0)partition(3)\WINDOW S
[operating systems]
multi(0)disk(0)rdisk(0)partition(3)\WINDOWS="Windo ws XP Pro" /fastdetect
multi(0)disk(0)rdisk(0)partition(3)\WINDOWS="Windo ws XP Pro X" /fastdetect /kernel=c:\cygwin\cygwin.dll
To make your "X" as the default, I believe you just need to change the order under [operating systems] to which one you want to boot first since they're both booting from the same partition.
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