It doesn't matter if you run it on Windows or Linux. The compiler was just optimized to run on Linux, therefore it can run faster on Linux. But the compilation itself won't matter.
I'd say it is time for you to go through your local NI representative to try to get some time with the NI Systems Engineering group. They will likely find plently of places to help you optimize and fit your code in into an FPGA.
There are only two ways to tell somebody thanks: Kudos and Marked Solutions Unofficial Forum Rules and Guidelines "Not that we are sufficient in ourselves to claim anything as coming from us, but our sufficiency is from God" - 2 Corinthians 3:5