<soapbox>
Any 3PP that forces one to use their (inevitably out of date) version
of cygwin (and thereby killing the official installation) is IMO broken
and the issue should be taken up with them. At the very least, it
shows they have such little faith in their own software's robustness
that they won't risk it running on an newer version of cygwin.
Imagine the chaos if ALL software was installed like this. You might
end up with 100 different versions of cygwin on your PC, and ProductA
would never be able to talk to ProductB because they'd need two
different sets of registry settings simultaneously.
I'm sure their justification is that they are reducing support costs by
ensuring it's running on a known platform. Only if their customer
support is forced to resolve the problems caused by their installation
will they learn that this is a false economy.
</soapbox>