M files and exe build problems

Hello,
Pleae help because this has been driving me crazy!
I am using a series of mathcript nodes to call up 4 x m files. Those top level m files also calls up other m files. But under the dependencies list of the Project Explorer, it only lists the 4 x top level m files. Anyway, it all runs fine but when the exe is built and ran, it by passes the m files functions without any error report.
When the exe is built are ALL the m files compiled or just the ones on the dependencies list? Do I need to include the m files in the directory of the exe file?
The run time engine has some unsupported mathscript functions, how do I find/filter out unsupport functions in the m files?
Is there anything else I need to check to get the exe file working properly?

I am sorry - I have not done much with mathscript nodes yet.
I had a look in the Labview help and it says this:
http://zone.ni.com/reference/en-XX/help/371361E-01/gmath/mathscript_node/
"The LabVIEW Run-Time Engine does not support
MathScript Nodes with warning glyphs. If a VI includes a MathScript
Node with a warning glyph, you must remove the warning glyph from the
MathScript Node before you build a stand-alone application or shared library.
The LabVIEW Run-Time Engine also does not support certain MathScript
functions. To include a MathScript Node in a stand-alone application or
shared library, you might need to modify scripts that contain these unsupported functions."
One of the things that causes the warning glyph is the use of include functions. So it seems you can't do this under the run-time.

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