There are some rules that are often broken with Initiator/Target and also with Disk/Tape Initiator ports.
NetApp/Partner SEs have an updated fc rules powerpoint in the net2 download and I submitted some edits a while ago...a great document and summary below
1) It is ok to have initiators mixed onboard and expansion slots
2) Expansion cards are hard set as initiator or target, but onboard can be swapped (already mentioned)
3) It is not ok to mix Targets onboard and expansion slots. Either all onboard or all expansion slots for targets
4) It is ok to mix port speeds on the same card or asic
5) You cannot put ports on the same expansion hba ASIC (1a/1b for example) to both disk and tape (1a to disk and 1b to tape for example), but you can put
disk on 1a/1b and tape on 1c/1d. However, if onboard ports it is OK (0a disk, 0b tape)...

This rule is often broken since it works but is not supported on expansion hbas. (kb22038)