I've seen this issue happen in both Windows.Forms and Delphi (native windows) based applications, caused by the interaction of "stay on top" with the Windows API.
Essentially, marking a form as TopMost
makes it stay on top of some windows, but not others - Window management has more than two distinct levels.
What I found is this: my applications would behave themselves when run normally, with tooltips showing on top. Problems would occur when switching to- and from- other applications - somehow the "TopMost" of the windoww would become "very-ultra-top-most" (non-technical term ;-) ) with the tooltips appearing behind the window.
Having described the problem, I'd like to offer you a solution - but I never did find a good one. Sigh.
Hope that the additional information will be enough for you to find the solution you need.