Are the files being reported as copied but not really getting copied? Do you definitely have 'Do not copy' on the Options tab unchecked?
There was a problem with the last build regarding exclusions, which was just fixed. Please download and install the beta again, and if any of the problem(s) persist, ZIP and post/send a .bld file that demonstrates the problem (creates folders/files as needed and copy step that reproduces the issues) and a build log file. Thanks.
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