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Hi Gavin, currently the latest release of ArcGIS is version 10 so I think maybe you mean ArcGIS 10 with service pack 2?
You're correct that ArcLogistics 9.3 can't be installed on the same machine as ArcGIS 10 but there is an ArcLogistics version 10 as well which is compatible. You should contact your sales rep. for more info.
Other workarounds also exist including running a virtual machine on the host computer so you can have 2 completely different environments but this starts getting a bit more complicated.