Hi Mauro,
Sounds like a problem with your libraries; you probably have the Commodore 68040 library installed.
68040.library should be small in size, about 1 block. (It's a "fake" library, which loads the needed 68060 library.)
Later versions of setpatch (I don't know when it started, but 44.38 at least) load the 68060 library directly, and don't need an '040 lib.
About the CLK jumper -- set to 040 is OK, all this does is cut the RAM speed in half. (At 50 MHz, the CPU runs at full speed, while the RAM runs at 25 MHz.) The card is picky about RAM, and sticks that run at 50+ MHz are somewhat rare.
If all else fails, I can email you a working install disk, just let me know.