The biggest differences between the two products is around monitoring and troubleshooting. Boxtone is focused on monitoring and does that really well, but is not focused on troubleshooting. As a result, a user will get a series of alerts when a piece of the infrastructure goes down and will use their own experience to try to identify the root cause of the problem. Zenprise on the other hand automatically correlates these monitoring alerts, provides the root cause of the problem, and most importantly, provides detailed step by step resolution instructions on how to fix the problem. If you're looking for a tool that will do troubleshooting for you and tell you how to proactively fix problems, take a look at Zenprise. You can find a demo of the product at: Zenprise - Proactive Troubleshooting for BlackBerry Enterprise Server. Resolves BlackBerry Infrastructure problems, Supports BlackBerry 4.0 and higher.
The other big difference between the products is the degree of depth in identifying issues in Exchange or Active Directory that could cause problems with BES. Zenprise will actually look at configurations (as well as errors in the application log and performance issues with SNMP/WMI data) to identify things like when patches applied to Exchange break BES (e.g., patches that change dll versions on Exchange), when permission changes occur within AD on the BESAdmin account, when DNS records are incorrect & prevent name resolution to the SRP network, when a user's password in Active Directory has expired, etc.
Bottom line, they're both great products, just depends on what you're looking for.
[Full Disclosure] I'm a Zenprise employee