upgrade + fields settings = broken forms?

I hope (and suspect) I've done something ignorant, and not found a new bug.

While using 1.10 and earlier, I had customized the field settings - the common ones, and also for each publication type I used. I made some that were visible, not visible, changed whether some fields were required, etc. and changed a lot of the weights. It was all working nicely.

After the upgrade to 1.13, I went to the creation form for a 'Report' type, and noticed that a couple items I knew I had set to visible, (publisher and place_published) were now hidden in "Other Biblio Fields". I was able to create the biblio node OK, but went to check my fields settings for common and 'Report' type. I don't think they had changed from before, I thought, "weird, why are those fields now not visible? Maybe the upgrade doesn't respect my settings." I decided to save the 'Report' type's field settings (without changing them at all) to see if that would force them to be used. Well, after that, the entry form is completely borked for the 'Report' type! Some fields (like Year, Authors) are missing, and some (like Title) now have two or more text boxes.

So now, my questions are:
Is there some warning or documentation I've stupidly overlooked, regarding field settings and upgrading?
Should I reset all the field settings to defaults and configure them all over?
I have some custom types, created and configured before the upgrade...what will happen to them?

My apologies if this has been covered already and I just couldn't find it.

Thanks!

foraker