DNN and Fallback Skin Doctype

Recently I was required to upgrade a customer's DNN site from 4.8 to 5.0. Simple enough, right?
1) Copy site folder to another location
2) backup database
3) extract the contents of the upgrade zip file into the site folder
4) navigate to http://SITEURL/install/install.aspx?mode=install
5) VOILA! Upgrade complete

Unfortunately, after doing the upgrade the customer's dropdown menus were no longer appearing on top of the content (we had used CISS.SideMenu for the menuing system) . Upgrading the menu module only made things worse - the menu bar disappeared altogether. So, I reverted back to the 4.8 site and went about replicating their environment on a VM.

Thinking that maybe the problem was DNN 5.0 I decided to go straight to DNN 5.1. The upgrade was successful and in the process I was able to resolve another problem the customer was having - the dropdown menus look garbled in IE 8 unless the site was run in compatability mode. I was stoked and ready to tackle the production server again.

Much to my dismay, after the second upgrade went seamlessly, the same problem appeared. I was ready to throw in the towel. Thanks to a kind co-worker who jogged my memory I was able to resolve the problem.

I had changed the Fallback Skin Doctype on the portal settings screen to XHTML 1.0 transitional on my VM AND on the production server BEFORE doing the upgrade (http://www.dotnetnuke.com/Community/Blogs/tabid/825/EntryId/2130/The-Fallback-Skin-Doctype-and-skinning.aspx). This had been done in an attempt to resolve the IE 8 issue. Unfortunately, the upgrade to 5.1 wiped out this setting. Once I changed it back the menus appeared just fine.