I had the exact same problem. I would RDP into my work computer to work in NetBeans and pasting would not work. I found a simple, although annoying, workaround: before pasting, switch to another application like Notepad or whatever you happen to have open, then switch back to NetBeans. That's all. You don't have to paste into the other app, just switch to it and switch back, then you'll get the current clipboard data... at least I do.
I also use Chrome but have not noticed that it makes a difference if it is open or not. Although if you close it before pasting, you have switched to another window and then the paste will work... but of course that will work if you close any other program.