Hi,
I am having the same problem. What kind of information is needed to reproduce it on your side? The complete project might be a bit huge, and I don't want to disclose it either.
Attached is the .cproject file of the project in question. This runs fine in CW 10.4, but with CW 10.6 on my colleague's machine I get multiple makefile entries for SmartLED-III.elf. The first one seems OK but the latter two are empty, which obviously causes the build to fail. As soon as I remove the pre-build entry, the build works in CW 10.6, too.
As CW 10.6 refuses to work on my machine (Java crap again?), testing may be a bit slower, though...
Best regards,
Wolfgang