I can repro it now, thanks. After looking into it, we may be in a pickle. Basically SyntaxEditor (our custom code editor control) is used as the code editor here. We implement some code to allow the keyboard to show when its tapped for focus.
I think what's happening is that when we call the Windows Save dialog, the dialog is telling the soft keyboard to switch to a certain "input scope" (think of it like a hint for what keys should be enabled and show) that is appropriate for file names. Standard TextBox controls have an InputScope property we can set but that does us no good here since our control is custom and doesn't inherit TextBox. I've been searching the WinRT framework Microsoft provides to us and unfortunately don't see anything that looks like it would help either.
My next step is to context some folks in the text/input team at Microsoft to see what options are.
I found a workaround for when you get into this mode. Slide out the charms and click the Search charm. The TextBox there will tell the soft keyboard to return to "normal" input scope and it seems to carry over into the app too.