There still are search path problems in 4.6.1 on Mac (not tested on Win).
All applications with MaxMsp are searching outside the application bundle for different files.
Very easy test :
1)create a patch with [mxj help] and [standalone] inside.
2)create an application from it.
3)copy the app in a folder
4)copy mxj.jar in the sasme folder (not inside the application bundle)
5)launch the app, you see that the application has taken the max.jar from outside the application :
Stalwook:/tmp kristof$ ls -d /tmp/bug-path-mxj.app /tmp/max.jar
then, in max status window :
MXJ System CLASSPATH:
(mxj classloader) dynamic classpath entry /private/classes/ does not exist.
• error: Could not load class 'help'
This is a very annoying problem, because when you put your application in /Applications folder, then it may take 5 minutes to start (it will scan everything looking for its files).