Manipulate slider unresponsive after suspend in Linux
I've also noticed this bug, although buttons/drop down menus do continue to work, for me only sliders become unresponsive after suspend (Ubuntu 12.10/Mathematica 9.0.0.0 x86 64 bits).
A possible workaround is thus to change all parameter controls to buttons/dropdown menus by providing a finite list of values the parameter is allowed to take:
Manipulate[Plot[a x, {x, -3, 3}, PlotRange -> {-1, 1}], {a, Range[-2,2,.5]}
Let's hope someone at Wolfram notices this thread! Have you already filed a bug report?