This may simply be a Remote Desktop Connection bug -- I believe Lion isn't fully supported yet -- but here's the problem. I'm using Microsoft's Remote Desktop Connection and everything's awesome except I can't save programs with ctrl-s. What actually happens when I hit ctrl-s is the window shows a small bit of space at the top (about the size of a menu bar, coincidentally) and I have to hit Command-2 twice to get the window back to the correct size. I think the program thinks I'm trying to save a connection. Sadly, I can't see an obvious way to remap that particular shortcut.
I had this issue too -- you can rebind the Save function of the Remote Desktop application in OS X's Keyboard menu. Just open up Keyboard, navigate to Application Shortcuts, and add a new mapping for the Remote Destkop Connection application to map Save to another key combination (I used Command+S).