I have a card that mirrors this one from your list:
Retail name: SATA300 TX4
Chip label: PDC40718-GP SATAII300
Vendor-Device number: 105a:3d17 (rev 02)
Through testing, I've found linux 2.6.16 and 2.6.17 find the ports in this order (the list is ordered by linux detection):
1. silkscreen port 3
2. silkscreen port 2
3. silkscreen port 4
4. silkscreen port 1
NOTE: the patch I have submitted ( http://marc.theaimsgroup.com/?l=linux-ide&m=114082978311290&w=2 ) is a solution that doesn't know about the older Promise SATA controllers, which are not affected with the "new wiring" problem, so the older controllers will appear screwed if you use it.
Hopefully we will collect enough info about all the SATA Promise controllers to distinguish the new and the old wiring controllers, then produce a new patch that will be a correct solution to the "new wiring" problem.