You are trying to pass a "/cygdrive/..." path to a tool which is completely unaware about Cygwin. Resolution of Cygwin paths (such as absolute paths, paths passing /cygdrive, etc...) is performed somewhere inside a cygwin dll library and all Cygwin programs are linked to that library. So only cygwin programs can access all the variety of paths. Other (native Windows) application may work fine with relative paths (because they are same in Windows and cygwin) but not with absolute paths.
There are several possible solutions:
1. Compile your own Cygwin-aware java and use it inside cygwin instead of windows-native java.
2. Change directory to a directory with a build file and use only relative paths.
3. Convert "cygwin" path to a windows path. Read Using Cygwin effectively with Windows chapter of Cygwin documentation. There is even an example related to java (read the article carefully, you have an issues with a CLASSPATH too).