Yeah, you might benefit from doing Micro Focus Adjust aka MFA with that lens... (has to be done on each camera, but the amount of adjustment you dial in will apply to any 50/1.4 you fit to either camera... it's camera specific, but not lens specific).
Canon recommends setting up your MFA target at a distance 50X the lens focal length, as measured from your "film plane" mark on the camera. That would be just over 8 feet with a 50mm lens (50x50=2500mm or 250cm, or approx. 97 inches).
Canon's recommended method is to put the camera on a tripod, focus the lens on a good target using One Shot and just the center AF point, then switch to Live View and - while watching the distance scale on the lens - activate focus again. If the scale moves at all, then you need to dial in some MFA and retest.
The idea behind this mehod is that standard AF uses Phase Detect focus, while LIve View uses a completely separate, slower but generally more accurate Contrast Detect focus. If you dial in the standard AF to match Live View AF, you should get pretty accurate focus. This mehod allows you to use a simple target, just about anything flat with some detail on it that gives AF something to lock onto, and not have to fool around with buying or making or setting up special angled targets and reading scales.
It's a lot easier to use with a prime lens than with a zoom. With a zoom you sort of have to do it two or three times, at different focal length settings and distances to the target, then often will have to average the amount of adjustment you dial in with MFA (unless you use the lens most of the time at one particular focal length, want to bias it to be optimal at that focal length, and don't mind if there's more error at other focal lengths).
At f5.6 your 50/1.4 should be nice and sharp.
Use f2.0 with some caution... It will be sharper than f1.4, but still likely will have a little bit of softness. I usually try to stop down at least to f2.2, but f2.5 or smaller is even better.
At the other extreme, using 50D try not to go beyond f8 or f11 at the smallest, or diffracation will start costing some fine detail.
Are you using any filter on the lens? If so, be sure it's a good, multi-coated one... or just remove it to get optimal sharpness.
Are you using a lens hood? It's rare, but possible for oblique light striking the front of the lens to effect AF. A hood can help (and the 50/1.4 in particular benefits from storing it with hood reversed, to protect the focus ring from getting bumped... which can damage the AF mechanism).
Second shot, and perhaps the third, was fill flash used? Was the flash focus assist turned on?
50/1.4 is usually pretty accurate focusing... If you continue to notice problems, might be worth sending it to Canon to be checked. It might just need calibration. If the AF system needs to be replaced and the lens isn't under warranty that might cost around $160, just guessing from what I've seen in the past.
Ah... just saw your followup... Since you can't MFA to get both near and far to focus right, it's more likely the lens needs to go in for calibration. I'd run the same test on both cameras, just to be sure. If it does the same on both, send the lens in. If it only does it on one camera, then it's more likely the camera is off somehow.