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Having a problem with Max Runtime 4.6.1.

We have a large patch which when loaded within 4.6.1 editing environment
works as expected. No issues when editing the patch, however, when running
the patch on the same machine within the runtime for 4.6.1 our patch does
not find its referenced subpatches.

Our directory structure is

Main Patch
Code/subpatch1
Code/subpatch2
Etc.

We have defined the search paths through the File Preferences as well as
through the filepath object. The runtime cannot find the subpatches unless
they are placed directly next to the main patch.

We have also attempted to use the standalone object, to no avail.

If we launch max runtime and load the patch, the first time it doesn't work
even though sending the message ;max search paths tells us search paths are
indeed there. However if we close the patch without quitting Max Runtime,
the second time we load the patch it finds the subpatches.

Any ideas? Thanks,

James