I just wanted to put this on the list in case anyone else had a similar problem...  

I was running through the overo openembedded howto (http://gumstix.org/software-development/open-embedded/61-using-the-open-embedded-build-system.html), after setting up Ubuntu 11.04 under vmware, running on mac.  To try to keep my disk image from getting too big, I setup my home directory to be on my real mac partition, accessed from ubuntu via nfs.  

Everything was working fine until bitbake got to compiling perl-native (around package 30/5168)... I was getting lots of errors about there being no makefiles, which I was resolving by manually running the "Makefile.SH" scripts in various subdirectories of the downloaded perl code.  It finally looked like the problem was that I was doing things in a case-insensitive HFS partition... at one point the scripts were trying to create "Makefile" deleting another file "makefile", which of course ended up overwriting and deleting both.  

Final solution for me was to scrap that whole configuration and just do everything in the ubuntu image with ext3... perl-native finished compiling