Did you by chance disable Peripheral Illumination Correction? I believe it's enabled by default; see page 147 in the manual for instructions on checking it. Are you using any filters or a third-party hood?
DJL329 - how does this setting affect the vignetting and what would be the disadvantage of disabling the PIC?
PIC helps to brighten the corners on lenses that you have configured in order to reduce
vignetting. The corners should appear darker when that setting is disabled. You can test it out by setting up on a tripod and take 2 identical shots -- 1 with it enabled, 1 with it disabled -- to see the difference. Note: it is a per lens
setting, so turning it on or off for your 50mm lens, would not affect whether or not it is enabled for your 135mm.
I'm fairly certain that the EF 50mm f/1.4 is one of the lenses that is ON by default. I thought that perhaps
disabled PIC for that lens, which could have caused
the vignetting that you are seeing. If you have not
disabled it (you need to attach the lens to the camera to check), then that's probably not the issue.
Try uploading (or posting a link) to a couple of sample images, so we can check it out.