The CLASSPATH for Eclipse isn't taken into consideration when debugging apps inside Eclipse. That's a completely different classpath, based on the project's classpath PLUS the debug session's classpath. You have left out some details, but from the sound of it, you're trying to debug and not getting the driver. You need to add the driver jar to the debug session's classpath. The Run/Debug Configurations menu will permit you to retrieve and edit the debugging profile, including its CLASSPATH.
Just for info, I was REALLY disappointed in the Microsoft SQL Server JDBC driver. I inherited a monstrosity where half the program's application logic was in stored procedures with transaction nesting all over the landscape. The Microsoft driver had a complete nervous breakdown. I switched to an open-source SQL Server driver I got from SourceForge and the problems went away.
An IDE is no substitute for an Intelligent Developer.