canine behavior problems in crate

Question
I have a female maltipoo who is almost 3 years old.  She has been sleeping in her crate every night since we got her @ 8wks.  We also have an 8 year old male beagle who's crate is next to the maltipoo's crate so she knows she is not alone.  We have not had any trouble with her crating up at night until the past 3 months or so.  We feed our dogs at night in their crates (so that the beagle doesn't eat all the maltipoos food), so they both are very willing to get in their crates at night.  But recently, after our maltipoo is done eating she starts scratching in her crate like crazy.  We have a towel in the crate, but that does not help.  I have let her out to go to the bathroom, but she never needs to go and doesn't want to go back into her crate after that.  In the past week, she has started barking as well as scratching.  Last night she barked off and on for over an hour.  I am not sure what to do with her.  I don't want to leave her out of her crate at night because we travel to see family quite a bit and the dogs must stay in their crates at night when we are at our family's home and anytime no one is home.  Do you think this separation anxiety?  What should I do?

Answer
When you say "scratching in her crate" I assume you mean she's scratching the CRATE pan, itself.  This sounds like a barrier frustration problem.  Something may have frightened the dog when she was confined and you were not present; it may have been a storm, a sudden backfire outdoors, etc., and may be linked to the lack of light outside (night time).  You seem to be REWARDING the behavior by paying attention to it.  Dog scratches at bottom of crate; owner opens crate door and lets dog out; this is a chain of reward. Do not confine your dogs in their crates until AFTER they have been outdoors for the last time prior to your retiring for the night.  Then IGNORE whatever the dog does for a few nights.  If this has been ongoing for three months and you have been giving her your attention (and release from the crate, to boot), it might take a week or two but the behavior should self extinguish.