Controls locking up while in space

I am trying to launch a space probe which involves quite long periods of waiting at times to be able to raise apoapsis maximally. Sometimes during these waits when I try to start up engines again (or do anything really) I can't get it to work. Nothing happens. I can't toggle RCS or SAS, I can't change throttle or extend solar panels.

How can I get out of this frozen state and why does it happen? Is the distance from Kerbal to great and no signals can reach the probe?

Your probe is probably out of power. Unlike manned capsules, probes don't have any internal way of generating their own electricity.* You need to add solar panels (and remember to deploy them once in orbit), or Radioactive Thermal Generators to your probe. Running most chemical engines also generates power (which is how you can get into orbit), but due to limited fuel, this is typically impractical.

If you're using solar panels, you may also want to consider strapping some batteries to your probe as well, especially if they aren't going to be in direct sunlight all the time.

Unfortunately for you, your probe is basically dead. The only way to resurrect it would be to dock something else to it for power generation, but that assumes that a) you have a docking port on the dead probe and b) it's worth it to even do that.

^{*The first part isn't exactly correct, since manned capsules don't actually produce a net amount of electricity, however they don't consume it either, and when you're out of electricity, they still function and now (as of version 0.21) consume electricity when their reaction wheels are used to change orientation.}

are you still in time warp? setting any degree of time acceleration locks out all controls for safety.

KSP Control Locked Checklist:

• You must have electricity (check resource panel on the top right of the screen)
• You are not fast forwarding (press / key to stop any time-warp)
• If manned probe:
  • You have an astronaut in a "command module" of the ship (either a pilot, a scientist or an engineer, sitting inside a command module, not in a passenger module)
• Or, if unmanned probe:
  • You must have KerbNet access (check on the top left of the screen, next to mission time). Depends on difficulty setting, you might need a relay network if you are too far from Kerbin or if the Kerbal Space Centre is not directly facing you.
  • Make sure your probe is not in "hibernation" (right click on the probe module to check).
• Sometimes the control locks up due to glitches (especially if you have mods), try reload the save.

And finally, the real reason I wrote down this answer, because I did all above check and it still didn't work...

• This spacecraft is not marked as "debris" (right click on the probe module, rename vessel, change category back to "Probe").