Jim H WY on the IPF5000 Wiki came up with a solution to his nasty banding problem for the trailing 1.25 inches of paper on prints made from the Cassette. It completely eliminated the banding for me as well, so I feel reasonably confident that this fix is the solution. Here is the procedure (see the Wiki for additional details and discussion):
1. Install Firmware 1.23
2. On the printer LCD menu choose: Adjust Printer -> Manual Band Adj -> Adj Far Ed Feed and set to "Yes"
3. You can use letter size paper in the Cassette. Printer will print a sheet (assuming you have paper in the Cassette and have the Cassete selected)
4. Examine the rows C1 and C2 with a loupe and find the column in each row that shows no banding. If you can't choose between two adjacent columns, use a number between them.
5. Enter the number determined above for C1 and C2 by using the right and left arrow keys and choosing OK.
You may need to make this adjustment for every type (and size?) of paper you'll be using, and you may need to make it every time you switch paper because the printer does not appear to save these parameters separately for each paper type/size. You can record these values for each paper type and if you have to re-enter them, just print the pattern on a blank sheet 20 lb. bond paper so you can get to the part where you enter the values for C1 and C2.
It isn't known yet whether the Automatic banding adjustmehnt would work just as well, or how different the values may be for different paper types. More information is needed from Canon about how the values are stored and whether they apply to each paper type or the printer as a whole.