I am getting a similar error.
WARN util.Utils:650 Exception extracting jars into temporary directory : java.io.FileNotFoundException: C:\Tomcat5.5\temp\_axis2\axis232336axis2-1.3jar (The system cannot find the file specified) : switching to alternate class loading mechanism
The error repeats every so often. Moreover, I am seeing a new axisNNNNNNaxis2-13.jar file being created every couple of seconds. The web applications within Tomcat are still working, but still, this is not a good situation.