When it came to compressing a 2GB file using Gzip, it was noticeably faster with the real Ubuntu 10.10 installation to an EXT4 partition rather than to the EXT4 file-system within the disk image that is in turn on a Windows NTFS partition. The standard install took nearly half the time that it took Ubuntu 10.10 installed by Wubi to compress this example file.
With CompileBench, the disk write speed was 23% faster when installed to a partition rather than Wubi.
One configuration is faster than the other with FS-Mark is, but this time it is the Wubi installation that is running much faster. Yes, in this particular test, where Ubuntu 10.10 is residing on a disk image within a NTFS partition it is actually faster. These results were just gathered yesterday so we have not explored all what is happening, yet, but this is not the only test where this situation occurs. The situation though does appear similar to the disk problem we exposed last year where when running Ubuntu within a virtual machine some disk operations are running much faster than when executed on the actual drive, as sync guest calls are being made a-synchronously or are being cached. We talked about this problem in The Five Stages of Benchmark Loss at this year's Southern California Linux Expo.