This is an annoying issue I ran into today with remote desktop and windows. I use remote desktop to get to my other computer at work and without the copy paste function it is a huge hassle. I found another blog that ran into the same issue to solve this issue:
Go to the remote computer, run taskmgr.exe then end the process rdpclip.exe then go to run and re-start the rdpclip.exe process.
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