Troubles with automake V1.4+cygwin (maybe perl related?)

[Wolfgang Liebich]

Hi,
I'm in the middle of porting a rather large *IX program to WindowsNT.
The porting per se is done, the program works. The only problem I now
have is that I've two sets of makefiles - the automake files for the
*IX-Ports and the VisualStudio .ds?-Files for WindowsNT. 
That's rather cumbersome, I would prefer to have unified makefiles. So in
order to get the autotools working I downloaded CYGWIN (latest version) 
with automake V1.4/autoconf 2.13. Yes, I do know that the new version is
1.5/2.5, but I have not come around to install the latest automake/autoconf
versions on the UNIX systems I'm working on.
The problem with the cygwin tools is - the makefiles come out scrambled.
The Makefile.am contains some conditionals, and they stay in the source
code verbatim; the list of the source files is intermixed with the
list of .PHONY targets - it looks bizarre.
It looks to me like some sort of CR/LF problem - the makefile.am's *will*
have CR+LFs, b/c I'm using PVCS for source control. But I've installed
CygWin with "Default Text File Type DOS", so it should not be a problem,
right?

I don't know if this email is on topic for this group, as it might be more
of a CYGWIN problem, but I hope that at least someone reading this mailing
list has some experience with CYGWIN.

TIA,
Wolfgang Liebich