I use xclip every day and have no complaints. Until recently when I tried to paste into java app. You can fire sample java text field from this page:
http://download.oracle.com/javase/tutorial/uiswing/components/textfield.html (click on Launch)
What I tried:
1. Filled all 3 buffers (p, s, c) with a text, pasting in java is not possible (remember to use Shift-Ins)
2. Watched the xclip -o after copying from java app (Ctrl-Ins): p and c got filled. xclip --selection secondary remains in active processes.
3. Copying/pasting between java and other windows (e.g. gedit, firefox) works like a charm
I am on Debian Linux with openbox. package xclip melds 0.08-8 (xclip itself has no --version option).
Do you experience same problems in your environment?