When doing a CD upgrade from 5.8.6 to 5.9 the installer
found garbage names for my partitions (looked like
it might be a bad pointer or similar) making upgrading
impossible.

The amount of partitions was correct and a normal install
works fine.

The upgrade was attempted to a SCSI disk (aic7880) from IDE
cdrom. One special feature of the disk is that it was
partitioned under a different scsi controller, so fdisk
reports errors like

/dev/sdb1             1      102   103849+  83  Linux native
Partition 1 does not end on cylinder boundary:
     phys=(24, 133, 62) should be (24, 63, 32)
/dev/sdb2           102      167    66464   82  Linux swap
Partition 2 does not end on cylinder boundary:
     phys=(40, 133, 62) should be (40, 63, 32)
/dev/sdb3           167      820   668794   83  Linux native
Partition 3 does not end on cylinder boundary:
     phys=(201, 133, 62) should be (201, 63, 32)
/dev/sdb4           820     4134  3393818    5  Extended
Partition 4 does not end on cylinder boundary:
     phys=(1018, 133, 62) should be (1018, 63, 32)
/dev/sdb5           820     2869  2097769+  83  Linux native
/dev/sdb6          2869     4134  1296047+  83  Linux native

because the geometry used is different, but the disk has
worked like that without problems for a year or so.