As it took me a while to figure this problem out I will post this here to help those who are experiencing the same problem.
Although old third-party peppers run on Mint v2 most of their panes cause major flickering issues when displayed causing Mint to become unusable for a few seconds after every action (Page loading, button clicking, etc.). Until the peppers have been updated to work on the new version of Mint the only possible solutions I have found is to either hide the panes (The pepper will still record information however) or just put up with it.