issue since swapping internal ports of backup drives

Since both swapping in replacement hard drives, and swapping the (internal) SATA ports of the Destination hard drives, for my two Backup Jobs, the Incrementals for one Job have begun taking much too long, sometimes as long as the base.  The Job never had this issue before.

(I *never* defrag except right before running a Base backup, and the contents of the Backup Source hard drives has continued not to change much.  Long ago here someone here advised me that Restoring an image might be problematic after such a "drive architecture" change, so I noted well when I swapped ports in case I needed to do a Restore.)

I then tried Deleting the Recovery Point sets which were missing (because I'd shelved the hard drives they were on) from "Manage Backup Destination", but that hasn't helped.

What's best practice?  All I can think of to try next is to do one or both of:

1.  Delete and re-create the two backup jobs
2.  Go into "C:\Documents and Settings\All Users\Application Data\Symantec\Norton Ghost\History" and delete the files with extension = .pqh (Is that right, I forget, please remind me if it's instead of .policy files I should delete).

If hard drive/port details would help:
*Job One*
Source: WD6000HLHX (containing 209 GB), onboard SATA
Destination: recently changed from HDS721010KLA to ST31500341AS, plus recently switched from onboard SATA, to PCI SATA (SIIG SC-SA4011-S2).

*Job Two*
Source: HDS723020BLA642 (containing 624 GB), onboard SATA
Destination: recently changed from HDS723020BLA642 (because it developed errors as I noted in another post) to HDS723020BLA642 (yes, identical model), plus recently switched from PCI SATA (SIIG SC-SA4011-S2), to onboard SATA.

I upgraded the Destination Drive for Job Two to onboard SATA (and downgraded the Destination Drive for Job One to PCI SATA) this because Job Two's Base backups took most of a day (during which I leave the PC alone).  

*Job Run Times*
Before swapping internal ports of backup drives:
Base Backups of Job One and Two took 1/2 hour and 16 hours, respectively.
Incremental Backups of Job One and Two took 3 minutes and 6 minutes, respectively.

After swapping internal ports of backup drives:
Base Backups of Job One and Two took 1 hour and 5 hours, respectively.
Incremental Backups of Job One and Two took 6 minutes and <sometimes 5 hours, sometimes 1 hour, sometimes 8 minutes>, respectively.