Problem running through IDEs in Linux.

I have a really weird issue. I'm a beginner and i work with simple .java files. I'm using Linux at the moment and i can compile my source and run file using java 1.5 from the terminal. I have a couple IDEs installed as well that i would like to use.
I've tried a couple simple Java editors: Scite and EJE (everyone's java editor) and both of them don't run the code properly. When they get to the console input part. Where i use the scanner class to get input the first one Scite throws NoSuchElementException and the second, EJE, doesn't show the println before the variable = stdin.nextDouble(); line.
Again neither of these problems occur from the command line. It's only when run from within the IDEs.
Please help. Thank you.

IDEs represent what you see in a console within their own panes. They do
this with varying degrees of fidelity - the cursor is sometimes not where
you would expect it, or new lines are not displayed until after new text
is written.
As no doubt others will tell you, it's a good idea to stick with a plain text
editor at least until you've mastered the "man page" for the java/javac/jar
commands.
On Linux I use Kate for text editing - it syntax colours .java files and has a
file browser off to the side. I use some program whose name I've
forgotton (!) to slide down a console screen when I push F12. Kate has
a built in console pane, but I prefer the console to use lots of screen space
when I want it, and none when I don't.
(Even if you don't use the K desktop, it's worth installing the necessary files
to allow Kate to work - unless others can suggest a better Linux text editor.)
Along with a web browser so you can get at the documentation easily,
you've got everything you need.

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