Thanks!
1. It should not be a problem as long as long as you were sending the passports to Ottawa from within Ontario. Scroll down to 3.1.1 in the link below to see what Canada Post classifies as a region. The attendants at the Canada Post outlets generally know what they are doing and are pretty good, so I wouldn't worry at all. I actually used Canada Post Priority (a faster version of Xpresspost).
http://www.canadapost.ca/tools/pg/manual/PGxpresspt-e.asp
2. Did you apply with the old passport and then subsequently get a new one? If so, did you then inform CPP-O about the new passport? Or is the old passport of yours really old and you never used it for the PR application? Generally, if someone applied with one passport and then gets a new one, it is recommended that s/he scan and email the new passport's copy to CPP-O. That way CPP-O has the new information on file. If you didn't do that, but included a cover letter with your mail (with UCI & Application # and the copy of the PPR email), then I think you will be fine cause the CPP-O should be able to figure out your identity with that information.