This sounds familiar. You're not running that inside a virtual machine, or in an RDP session, by any chance?
I'm not even sure if it's in RDP sessions or in VMWare virtual machines that I sometimes experience it, or both, but I *do* have noticed that the clipboard can be emptied unexpectedly.
Copy the same text to the clipboard again, even without re-opening the target window you want to paste into, and it (usually) works.
I think it happens -- sometimes -- when the focus is moved from one machine to the other and back.
I often have a VM or an RDP session (or both) running on one monitor with the other still used locally. Moving the mouse from one screen to the other and back, without even clicking, can be enough.
Having non-text data (an image for example) on the local clipboard seems to make it worse, even to the extent that I sometimes have to clear the local clipboard (by copying an empty string) before I can copy text on the other one again.