It appears the lastest versions of Linux and Windows both enable TCP windows scaling by default. This in itself shouldn't present a problem and should improve connection speeds to sites as larger tcp packets can be negotiated.
If however the site you are trying to access if behind and old firewall or router then you might find after upgrading to Windows Vista or a recent version of Linux (Redhat 6 for example) that some sites either crawl along or simply fail. This doesn't necessarily mean your computer is at fault. It could be your router - when did you last flash the rom?
But it could mean that a firewall or router sat somewhere between you and the site is causing the issue.
If you want to prove that its tcp window scaling causing the problem you can turn it off and see if it 'solves' the problem. If it does I suggest you get in touch with the site owner and ask them to get their firewall or router upgraded. Don't forget to turn Windows Scaling option back on after!
How to disable in Windows Vista and Linux
See Wikipedia for more details
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