For your underline matter: go to your style manager in the administration panel and scroll down to the additional CSS field at the bottom of your Main CSS page of whichever style you're using. Insert the following and save the changes:
Code:
a { text-decoration:none; }
That should remove all underlines of every link. As for your second issue, I have no clue. Perhaps it'd be useful if you could link to the modification. You might also want to globally disable the plug-ins to check whether it's actually due to the modification you mentioned.