I think you and I are having separate issues. I tried to duplicate your issue using text from notepad and that seems reliable regardless what I do with the VM application windows. I can't get it to fail or give me the wrong content. Not that that hasn't happened. Many times I will paste clipboard text content and I get the wrong content, I just don't know how to duplicate.
My issue I think is limited to files and copy/pasting files from guest to host. Whenever I go to paste, if it fails the first time and I get a windows beep, it fails the second time, and no matter how many times I try to paste, it fails. This almost always happens if I copy the guest file and then I change the VM application window state (minimized,normal, maximized).
NOW, in some cases, after the paste fails, if I restore the VM application window, then reattempting the paste (without copying again), does then work and the file appears on the host.