What was the partition layout on the laptop? As benchmarks in some of your previous articles have shown, the early part of a drive is faster than later part (sequential transfer rate). With a constant areal density, data flies under the read/write heads faster on the outer larger-radius tracks.
This is a something that's hard to get right when benching win vs. lin on the same HW, since usually you have a fairly normal dual-boot install, and one has the advantage of the outer tracks.
It's probably not a big deal if you have two adjacent 10 or 15GB partitions, with a big data partition somewhere else.
Ideally you'd re-partition and run benchmarks with each system installed to the first few GB. To get reasonable numbers for I/O dependent tests, you could make a scratch partition that you reformat to ext3 or ntfs before running the tests. Then have I/O benchmarks do their work in that scratch partition). (or XFS, see my previous posts for XFS tuning

. XFS's delayed allocation means it doesn't start writing until you runs low on RAM, or it otherwise decides it's time to start. This means uninterrupted reading for longer = less seeks = faster.) This tests fresh filesystems, not somewhat worn filesystems that everyone will actually have after even a day of use, but usually it's not a big difference because most filesystems don't suck that badly when they're not close to full.
I thought Vista SP1 was supposed to fix slow file I/O. Oh, IIRC, that was just slow file copying when you do it via the GUI shell. So never mind, I guess either your partitioning really skewed things in favour of GNU/Linux, Vista sucks at the file-encryption workload, or it was CPU-limited and the older JVM on Vista loses on that code.