1) We were able to resolve the issue with the check run. I would get a preview of the checks, but when we printed them it would give a "nothing to print" pop up. I was able to get the run to print, and I would assume moving forward there should not be an issue. We have not yet done a start to finish check run since the upgrade.
2)The misalignment is in all my order action reports. It appears that it has something to do with the fact that my item numbers vary in width. They can be up to 9 characters with the format XX-XXXXXXX. Columns to the right of the item number vary based on the length of the item number. I can email you a copy of the report, but would rather not post it online.