Larstr,
I see your point, but VMWare Server is not a good starting point since it's not desiged for high speed. I am in agreement that the issue I've noticed is likely 100% IO Meter running on Linux rather than Linux itself having such a major disk random IO speed difference over Windows 2008R2.
I had 4 separate indicators of this issue.
2 client benchmark apps showed better results on Windows
1 database vendor benchmark showed signifcantly better on Windows (400%)
and IO Meter
At the start it was difficult to say all 4 indicators were flawed, it was much more likely there was an issue with Linux OS.
As of today I believe both my client benchmarks were impacted by the unrelated E5 issue I described earlier, bad timing since we already believed it was a Linux issue. The client applications seem to be Java throttled rather than IO, seems to be only using a single thread. They are still working on that, the E5 fix has helped but not solved it.
The database vendor gave me a new benchmark test this morning (hot off the press), I believe my feedback led them to discover an issue in their test because now it's "almost" as fast as the windows test.
and finally, we have confirmation that IO meter is having Linux issues.
Conclusion... hopefully my environment was optimized all along, other than the E5 issue which is now corrected on 1/2 of our servers.
I hope these notes help someone else in a similar situation - we've invested several hundred hours working on this in the last month.
John