H5DRead/H5DWrite extremly slow on Windows

I have a code that I have compiled and run on Linux. The code reads a dataset out of an HDF5 file that is about 60000 X 19 in size with H5DRead. It works fine. I can run it directly, or debug the code with eclipse and all is file.
I recently ported the code to compile and run on windows. Running the code directly works fine. However, if I use eclipse and run with the debugger, the single call to H5DRead takes over 4 minutes to return. Has anyone else seen this issue? I also see the same problem with H5DWrite trying to write the data to an HDF5 file. The write only takes forever when running in the debugger. I also ran the problem directly from GDB and see the same issue.
Thanks for any help.