Probably found my error: I was calling "gcc" instead of "ld" for linking step but did not add "-Wl," for the linker directives.
Now when using ld (i.e. in fact arm-eabi-ld) the alignment (in the elf file Program Header) is the same for Linux as for Cygwin. Maybe this answer can help somebody else facing the same problem I had. Cheers Philipp -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- Before posting, please read the FAQ: http://ecos.sourceware.org/fom/ecos and search the list archive: http://ecos.sourceware.org/ml/ecos-discuss