In the case of US Federal Bureau of Prisons, I suspect the actual reason is this: they have over 36,000 employees. When you have that many employees, an email migration project is not going to be cheap. Even at private sector prices, you are looking at a multi-million dollar project; then you have to add the usual federal contracting overhead. But, many other US government agencies used GroupWise too, and they all migrated off it–so very achievable if you have the budget.
Which is probably the real problem – does Congress want to appropriate US$X million so federal prison guards can have a better email system? They did that for heaps of other federal agencies, because those agencies made arguments "our staff will be so much more efficient at catching terrorists/reviewing licensing applications/whatever if we had better IT", and that convinced Congress to appropriate the money, and then the email migration funding came out of that. By contrast, BOP argues "better IT will make us more efficient at rehabilitating prisoners" and Congress goes "yawn, you think we really care about that?..."
Which is probably the real problem – does Congress want to appropriate US$X million so federal prison guards can have a better email system? They did that for heaps of other federal agencies, because those agencies made arguments "our staff will be so much more efficient at catching terrorists/reviewing licensing applications/whatever if we had better IT", and that convinced Congress to appropriate the money, and then the email migration funding came out of that. By contrast, BOP argues "better IT will make us more efficient at rehabilitating prisoners" and Congress goes "yawn, you think we really care about that?..."