Bad Cygwin

I am using Cygwin64 with all (I'm pretty sure) necessary dependencies. When using the netbeans IDE, I get a "Bad Cygwin" message telling me I need to reinstall cygwin. I procede to compile, however I get an error that Cygwin1.dll is missing. I tried to command-line compile, but I get the same Cygwin1.dll message. I have reinstalled cygwin numerous times, even trying the 32-bit version. Can anyone help, perhaps cygwin is not writing to the registry ??
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