I running Redhat AS 5 uname -a
Linux xxxx 2.6.9-55.0.9.ELsmp #1 SMP Tue Sep 25 02:16:15 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux

I have 2 EMC disks that are physically quite different in size and raid protection but to Linux they should just be devices. I partition them with the same script that using a 128 block offset (64KB) as recommended by EMC and of course the physical/logical beginnings are different, they always are. Both disks are working just fine, so why does one get this warning and the other not? What is fdisk trying to tell me?
Expert command (m for help):
Disk /dev/emcpowera: 32 heads, 62 sectors, 1008 cylinders

Nr AF Hd Sec Cyl Hd Sec Cyl Start Size ID
1 00 1 1 0 31 62 1007 128 1999744 83
Partition 1 has different physical/logical beginnings (non-Linux?):
phys=(0, 1, 1) logical=(0, 2, 5)
2 00 0 0 0 0 0 0 0 0 00
3 00 0 0 0 0 0 0 0 0 00
4 00 0 0 0 0 0 0 0 0 00

Expert command (m for help):
Disk /dev/emcpoweraa: 255 heads, 63 sectors, 17605 cylinders

Nr AF Hd Sec Cyl Hd Sec Cyl Start Size ID
1 00 1 1 0 254 63 1023 128 282824197 83
2 00 0 0 0 0 0 0 0 0 00
3 00 0 0 0 0 0 0 0 0 00
4 00 0 0 0 0 0 0 0 0 00

Expert command (m for help):

until you get a better reply consider (but do not do unless you agree that you have backups etc) a proposal.

I think (I do not know) that it is because one drive was a bootable drive and the other wasn't. And at some point in time, the naughty one was partitioned in non-linux to a different table set.

2) if you have no essential data....all data backed up....dd used to save mbr and sfdisk used to save any extended partitions blah blah blah....my proposal is

wipe both mbrs with the dd command eg
dd if=/dev/zero of=/dev/emcpowera bs=512 count=1 and same for aa

then repeat your fdisk command but

3) does this error occur in other tools like cfdisk or sfdisk?