According to ClipIt: how to use actions? : If you Right-Click on the ClipIt icon you will see the Preferences Item. But that is not true! At least not on my Ubuntu 18.04. I get a list of clips whether I right-click or left-click. I also asked the question on https://sourceforge.net/p/gtkclipit/support-requests/4/ but nobody has answered.
I also use Ubuntu 18.04 and ClipIt. At first i did config too many history items, and then indeed i had the same problem : at the bottom of the ClipIt list are 5 menu items (in order top to bottom) : Offline mode, About, Manage history, Preferences and Quit .. but they were not visible due to the config .. so i edit the file /home/$USER/.config/clipit/clipitrc and i changed items_menu=# to a lower number (mine is 18 max now, due to screen resolution and font size). If this was your problem, then here's how to solve it.
I also had the same problem with VMWare + Linux. I installed/updated vmtoolkits etc. Finally got the answer.
Troubleshooting:
Goto Preferences > History tab >
a) Deselect "Purge history after timeout"
OR
b) Put a larger value like 10 seconds for "Purge history after timeout"