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I have both -SA and -SE and run mostly the same software on each (both running on the same version of WinXP but on different hardware platforms). Only -SA exhibits the following problem:
After running a number of RO applications for a few hours, then attempting to start an application (e.g. DPlngScan) the app will not start due to an abort on data transfer. Killing another application (e.g. PipeDream) and then attempting to launch the first app is usually successful. This happens with other applications than the ones mentioned and doesn't appear to be associated with the order in which they are run. There is plenty of memory free (typically 150MB). Sometimes killing other apps does not allow the first app to run (for example, I just tried StrongEd and it refused to run until I rebooted.
OK, I'd generally accept that this is a RISC OS issue, but the version of RO (4.02) is the same on both systems and SA frequently exhibits the problem and SE never does.
Any ideas? Anyone else seen similar problems?

You say you have 150Mb free. But VirtualRPC-SA and SE running RISC OS 4.02 only support 128Mb of RAM (because that's all that RISC OS 4.02 will correctly support).
If you've configured VRPC to have over 128Mb of main memory then put it back down to 128Mb.