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I have had a similar experience when joining tables - 3.3 will work when 9.3.1 will not.
Best explanation I have heard from tech support is that 3.3 is "looser" regarding data quality/standards. Also, it's leaner and meaner than 9x or 10.
Thanks Tim for you answer.
Problem is a 9999-error code doesn't say very much, almost a needle in a haystack. My guess it's running out of memory. Maybe its runs on 64 bits computer with more memory, although I don't think this is a real solution offcourse. Also clipping the dataset in 2 or 3 parts to solve the problem is not a real solution (too much processing and so on).
We have also used the software "Manifold" which can handle the job quite easy.
Why are these kind of basic GIS-processing steps on large datasets not able in ArcGIS 10.0?