Just to add to this (as I'm running into the same problem) - it's incredibly erratic. Copy+Paste will work reliably within Geany itself, but pasting out to external problems doesn't always fail, just most of the time (it may work fine a few times in a row, and then just not work the next 10 times you try).
Windows 8 with VirtualBox running here, so it looks like VirtualBox is the common denominator (especially with https://www.virtualbox.org/ticket/16192). Unfortunately there's been nothing but radio-silence on VirtualBox's side for over 3 months now.
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