Are you doing RAW or JPEG? In-camera processing can vary a good deal across the board depending on what the settings are. Personally I've always preferred RAW, and some of the tests at DPReview show that the results from two cameras of the same class, even from different brands, are quite the same when shot in RAW and processed in say, Adobe Lightroom, ACR etc.
The image quality may differ between the 1DII and 40D not only because one has a bigger sensor, but because the 1DII also has lower pixel density and technically requires less lens resolution to produce an image. Each camera itself has a low-pass or AA filter which can also introduce softness into a photo.
I'm sure there's heaps of other factors involved, which I'm not knowledgeable enough (and can't be bothered) to go into. Bottom-line is: there may be some differences, but I expect the lens to perform similarly on the 1DII.
When we're talking about the super low-density 1D Classic or the 1Ds Classic however, both of which have rather weak AA filters, you may expect more crisp images from the same lens. In the past I used the consumer 28-105mm f/3.5-4.5 on the 1D Classic and they were some of the most crisp images I'd ever seen even when working in RAW. Sharpening of 3 in DPP was usually more than good enough.
EDIT: OK, you mentioned you were shooting RAW in the most recent post just as I posted. Ignore the bits in my post about them.