When I emerged emacs using "screen sudo emerge emacs," I couldn't ctrl-c or ctrl-z the running install. However, when trying to duplicate the bug using "screen sudo emerge -p world," I was able to ctrl-c the entire screen session, but unable to ctrl-z. Reproducible: Sometimes Steps to Reproduce: 1.screen sudo emerge foo (preferably a long emerge ;-) 2.try to ctrl-z the running merge 3. Actual Results: Screen did not respond to ctrl-z in any recognizable way. Expected Results: screen should have stopped, and I should have the command line back...
Do have multiple keyboard set in XF86Config ? If you do have and have set the option to control it through alt-shift or something similar then that is probaly the cause. I recently realized that my <ctrl>-<key> did not always work in X as I had that option set.
Can't look at this without any updated info. Please reopen if this problem persists.