You can get a ton more information using "readelf".
In particular, take a look at the program headers:
readelf -l program
Your BSS section is quite different than the standard one, which probably causing the warning. Here's what the default looks like on my system:
.bss :
{
*(.dynbss)
*(.bss .bss.* .gnu.linkonce.b.*)
*(COMMON)
/* Align here to ensure that the .bss section occupies space up to
_end. Align after .bss to ensure correct alignment even if the
.bss section disappears because there are no input sections.
FIXME: Why do we need it? When there is no .bss section, we don't
pad the .data section. */
. = ALIGN(. != 0 ? 64 / 8 : 1);
}
If an input section doesn't match anything in your linker script, the linker still has to place it somewhere. Make sure you're covering all the input sections.
Note that there is a difference between sections and segments. Sections are used by the linker, but the only thing the program loader looks at are the segments. The text segment includes the text section, but it also includes other sections. Sections that go into the same segment must be adjacent. So order does matter.
The rodata section usually goes after the text section. These are both read-only during execution and will show up once in your program headers as a LOAD entry with read & execute permissions. That LOAD entry is the text segment.
The bss section usually goes after the data section. These are both writable during execution and will show up once in your program headers as a LOAD entry with read & write permissions. That LOAD entry is the data segment.
If you change the order, it affects how the linker generates the program headers. The program headers, rather than the section headers, are used when loading your program prior to executing it. Make sure to check the program headers when using a custom linker script.
If you can give more specifics about what your actual symptoms are, then it'll be easier to help.