Blackhawker: just my personal feelings here; no experience (yet) with the cannelure tool. I do understand what you experienced to be a common occurrence, though. My feeling is that unless you're running your loads on the very ragged edge of safety already, then having a small area on either side of the cannelure enlarged by .001-002" probably isn't going to hurt anything. The enlarged area will be swaged down to groove diameter once it gets into the bore anyway. Unless you're shooting bullets a whole lot harder than Linotype, I personally wouldn't lose any sleep over it.
To be on the safe side, download a few rounds and test fire them. If no issues present themselves, work back up to your original load while observing carefully for pressure signs. Use your chronograph if you have one to give you an indication on what's going on.
I bet you'll be just fine.