I actually tried running it via command-line and it worked perfectly. Then, I realized there was an issue with ImageJ not saving the PGM as 8-bit. I tried to create another wrapper based on your code which forced ImageJ to convert the image to 8-bit but it didn't work either. There seems to be a problem with the way the input/output streams. However, I managed to create a simple wrapper that uses BoofCV for the SIFT extraction since I'm on a tight schedule.
I'm using JDK8. Latest version. Eclipse environment.
And, a huge thanks for this library but I wish it supported more features. I'm working on a genetic feature construction/selection algorithm and a generic feature library that supports multiple feature extractors goes a long way.