Why does Eclipse-CDT sometimes not run my custom builder?

I have an Eclipse-CDT workspace with开发者_开发百科 8 projects in it. 3 of those projects use an External Tool (builder) to run a Python script that generates a header file prior to building the rest of the code. (Debian Lenny/ Eclipse 3.2)

When I build, the script may or may not run. It seems totally random. After failing I can just restart the build and the script might run, without changing anything.

I configured the builder once in Project|External Tools|External Tools and then imported it into the three projects. Since it runs sometimes the path and working dir must be correct. I have it set to refresh only the project, and to run after Cleans and on Manual builds.

I'm using find to ensure the output is not being created somewhere else and to delete the output after each test.

What could be causing this?