Can you post the command you are running? In general, the "--sdk-path" option is only used to generate app command and has some issues when used in application calls. The way the compiler works is based on a classpath, so the command you are using will help clarify what you are running into.
I try to concatenate my src folder without to create my app with the "sencha generate app" command . The structure of my project don't match with the from from "sencha generate app" created structure. All my ExtJS logic lies in this src folder and I need compile to compress and concatenate all these, to save loading time and size.
Another useful thing is to use "sencha -debug compile ..." to get a log of the dependency scan to get blow-by-blow on what is being determined. This can be a lot of output but if you are looking for specific files you can always search to see where they show up.
I realize now my issue is that I was executing the sencha cmd against ExtJS 4.1.2 and not ExtJS 4.1.1a or ExtJS 4.1.2a ... I started from scratch with one of the 'a' sdks and everything seems to be working great.
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