Very good points Yanna.
With the 10.x auto entry/exit, dynamic instrumentation and I think deep entry point, you might see a growth in the number of entries in the auto probe log since these are when the autoprobe has detected other classes to instrument.
If your application server or your application uses byte code instrumentation or in memory class redefinition, then the auto probe agent might re-instrument the classes thinking they are new classes.
If you are using a 1.6 JVM (oracle or ibm) then look into the non-redef.profile and noredef.jar within the agent. The out of the box IntroscopeAgent.profile is setup for a 1.7 JVM and you really shouldn't use it for a 1.6 JVM.
Could you state which application server, version of application server, JVM vendor and version or if you are using .NET? That might help others understand the scope of this issue and also see if it relates to anything they have seen.
Hope this helps,
Billy