I was running into similar problems yesterday on OSX. I was not doing any pasting.
What I was noticing when this was happening was not that Env.getClipboard() was failing to update to the new contents of the clipboard, but in fact somehow Sikuli was keeping the clipboard from working. When it got into this mode copy and pasting from one app to another was not working until I exited the IDE. I could select text in an app, hit CMD-C, and try to paste into another app and it would paste the clipboard before I hit copy.
But, unfortunately I can not reproduce this behavior today.
I was running into similar problems yesterday on OSX. I was not doing any pasting.
What I was noticing when this was happening was not that Env.getClipboard() was failing to update to the new contents of the clipboard, but in fact somehow Sikuli was keeping the clipboard from working. When it got into this mode copy and pasting from one app to another was not working until I exited the IDE. I could select text in an app, hit CMD-C, and try to paste into another app and it would paste the clipboard before I hit copy.
But, unfortunately I can not reproduce this behavior today.