I'm searching for a solution to a similar problem and came across yours.
We're installing Max/MSP on a group of WinXP machines in a student lab. The college's PC security measures include hiding the C: drive from students' view. This is problematic for a number of things but I've managed to work round most of the problems. One thing I can't do (which seems to relate to your issue) is using mxj.
The students do have access to another local disk (D:) and I've put a java/classes folder on there. I have set up the config file with a path to the classes folder on the D drive and when the JVM starts up it reports this path in the max window. The mxj class also work perfectly fine. But when I try to 'viewsource' the Max window reports that that the path can't be found BUT the path it reports to be looking for has had the D: replaced with C:
the max window reports:
MXJ System CLASSPATH:
C:Program FilesCommon FilesCycling '74javalibjode-1.1.2-pre-embedded.jar
C:Program FilesCommon FilesCycling '74javalibmax.jar
C:Program FilesCommon FilesCycling '74javaclasses
D:Extra Program FilesCycling '74javaclasses
(mxj) Unable to locate C:Extra Program FilesCycling '74javaclasseswhywhy.java. Decompiling with JODE
• error: (mxj) Unable to decompile whywhy
• error: message: C:Extra Program FilesCycling '74javaclasseswhywhy.java (The system cannot find the path specified)
I've just tried it on another machine using much simpler paths (i.e. putting a 'classes' folder in the root of my H: drive) still the same problem.
This seems to be a mxj issue.
We're on Max 4.5.7 (the problem may be fixed in 4.6.2 although we need Pluggo which isn't updated to work with that yet).