Thank you for the link: that explained it. Basically it was the Arduino developers being little *******.
Like WestfW wrote on that issue, it was extremely convenient. Fortunatly I have been able to use "make" from 1.0.6 with the avr-gcc 4.8.1 compiler.
A slightly unrelated problem is that some Makefiles that work with Toolchain 3.4.5 will not work with Toolchain 3.5.0, because some tools have different flags (like, for example avr-size).
Today I've been trying to compile a firmware for a LCR/Component Tester, based on an Atmega328P, and it compiles fine with avr-gcc 4.8.1 (from Arduino 1.6.7), and Make from Arduino 1.0.6. Any other combination, including the newer Toolchain 3.5.0 (avr-gcc = 4.9.2) will fail to build.
Since I am on Windows 7, I just just used the JUNCTION tool to have the "utils" folder on Arduino-1.6.7\hardware\tools\avr tool, pointing to the one from 1.0.6.
Thank you for your help once more, fellows!