Has this been reported as a bug to Altera? Paolo.gai's post is from 15 months ago, yet we also just encountered this problem still in NIOS 6.0SP1.
It's amusing what goes wrong. When GTF_GENERATED is undefined the buggy line introduces a "-I" with no directory argument suffix. GCC then interprets this as an include directive using its space-separated syntax, and gobbles the the next valid -I<alteralib> directive as gibberish, thus removing the valid library path that ought to have been included.
I'm always loath to modify the system files for fear of breaking on the next upgrade, so we've worked around this problem by predefining GTF_GENERATED as ".".