Hi,
There're just 2 things you can do:
1) Disable IPv6 (if not needed) and exclude the program (and its path) from AV, Firewall and others.
2) If the point #1 doesn't help, you can't do anything else. The problem is the program itself, it probably uses some "old" call which can be processed by Srv 2k8 but slower than Srv 2k3.
I say this because I wrote a "dummy" program which opens a connection to SQL and shows results with graphs and so on... on Srv 2k3 everything worked fine, in Srv 2k8 it was simply painful. The problem was a f.... call of a routine that was "deprecated" by MS...