I've run into problems with objcopy mapping PHDRS into a segment from a file that did not originally map PHDRS into a segment. This only occurs when removing the last section from an object file on configurations with small MAXPAGESIZE.
I tracked the problem down to a FIXME in elf.c:5241
/* Only set up the segments if there are no more SEC_ALLOC
sections. FIXME: This won't do the right thing if objcopy is
used to remove the last SEC_ALLOC section, since objcopy
won't call this routine in that case. */