Edit: Maybe you can try a different theme?
No glass looks promising
Well, I know where this problem is coming from technically, but unfortunately I don't have a solution for it yet.
It is now common practice for fancy UIs to use the Aero features of blending the non-client area (frame and border) of their windows with the client area (controls such as buttons, location, quick access or search bars).
This works well when aero is turned on, but fails when aero is turned off.
But there is a way to draw fancy windows without aero: by turning off the non-client area and faking it.
If you turn off the non-client area, you have to do a lot of common window-related tasks yourself (resizing borders, drawing the toolbar with it's buttons, system menu, etc.) and as an extra quirk, windows without non-client area are always fully maximized.
Which would, as you can experience, suck for thunderbird, so how do they prevent that?
I don't know. What I do know is that they are faking it. Probably they look for some margin which explorer sets but bb doesn't or bb doesn't set borders correctly.
Well, with all that said I have no fix in hand.
Also last time I tried sylpheed, it sucked. Only allowed to either sync all of my +13k emails or show me none.