(latest from git/master)
I just ran the test suite using the latest and now we're down to 5 failures!

  # TOTAL: 2478
  # PASS:  2382
  # SKIP:  61
  # XFAIL: 30
  # FAIL:  5
  # XPASS: 0
  # ERROR: 0

  $ grep '^FAIL:' tests/test-suite.log
  FAIL: depmod
  FAIL: depmod.tap 50 - tru64 [long VPATH] make & remake
  FAIL: depmod.tap 84 - tru64 [absolute VPATH] make & remake
  FAIL: tap-bad-prog-w
  FAIL: tap-bad-prog-w.tap 2 - non-existent test is reported
  FAIL: tap-bad-prog-w.tap 3 - non-executable test is reported
  FAIL: tap-bad-prog-w.tap 4 - non-readable test is reported

Started looking, and this one may be easy to fix:

  make[1]: Leaving directory `/h/j/w/co/automake/tests/depmod.dir/tru64-long.d/src'
  make[1]: Entering directory `/h/j/w/co/automake/tests/depmod.dir/tru64-long.d'
  make[1]: Nothing to be done for `all-am'.
  make[1]: Leaving directory `/h/j/w/co/automake/tests/depmod.dir/tru64-long.d'
  + make clean
  Making clean in src
  make[1]: Entering directory `/h/j/w/co/automake/tests/depmod.dir/tru64-long.d/src'
  .deps/foo.Po:3: *** missing separator.  Stop.
  make[1]: Leaving directory `/h/j/w/co/automake/tests/depmod.dir/tru64-long.d/src'
  make: *** [clean-recursive] Error 1
  + result_ 'not ok' 'tru64 [long VPATH] make & remake'
  + set +x
  not ok 50 - tru64 [long VPATH] make & remake
  FAIL: depmod.tap 50 - tru64 [long VPATH] make & remake
  + cd /h/j/w/co/automake/tests/depmod.dir
  + not am_keeping_testdirs

Once you see the contents of the offending foo.Po file:
(the "\:" on line 3 is the obvious culprit)

  $ cat tests/depmod.dir/tru64-long.d/src/.deps/foo.Po
  foo.o: ../../this-is/a-path/which-have/quite-a/long_long_name/src/foo.c \
   ../../this-is/a-path/which-have/quite-a/long_long_name/src/foo.h
  ../../this-is/a-path/which-have/quite-a/long_long_name/src/foo.c \:
   ../../this-is/a-path/which-have/quite-a/long_long_name/src/foo.h:

tap 84 fails for the same reason.

Here's the full log.