Bug reproduced in V9.0.1 and fixed in V11.1
This bug affects every part of GUI which is wrapped with Deploy as well as every Cell/Notebook/whatever with option Deployed->True. So it will affect e.g. all dialogs. Keep that in mind if you care about details in your GUI.
In addition to answers the most handy quick fix is to add
BaseStyle -> {Deployed -> False, Editable -> False, Selectable -> False}
instead of Deploy or to replace Deployed->True, in appropriate places.
Here are two small examples:
-
Through[{Deploy, Identity} @ Graphics @ Table[
Tooltip[{EdgeForm@Thin, Hue[i], Rectangle[{0, 0}, {2 - i, i}]}, i],
{i, 0, 1, .1}
]]
-
Graphics[{
Dynamic[{
If[CurrentValue["MouseOver"], Red, Blue], Thickness@.05, Line[{{0, 0}, {.5, 0}}]}],
Dynamic[{
If[CurrentValue["MouseOver"], Red, Blue], Disk[{.5, 0}, .2]}]
}, PlotRange -> {{0, .6}, {-.3, .3}}]
You can put cursor over the Disk or Line. As you can see the Disk covers the Line, so you can only get:
or
But as soon as we add Deploy (Deploy@Graphics[...), the Disk becomes transparent to the "MouseOver" event, and we can get the following result (with cursor on the right place):
This behaviour is so unexpected, I'm tempted to call it a bug. This change in behaviour is huge!
In this context, Deploy as a quick and nice function seems to be unreliable. :/
The walkaround is similar like there: Delay of events detection dependent of “MouseDown” position. But I doubt the reason is the same.


or 

Graphicsexpression and then display the two separated graphics withShow. I would call this behavior a bug. – m_goldberg Mar 09 '14 at 21:35