Hey @tomekwsrod – thank you a lot for your message.
I just finished my tests on a clean WordPress installation using the Twenty Twelve theme and everything works as expected there. The widgets are visible at my end even after activation of our plugin (Tested with Frontpage widget 1 & 2.
In case you have more plugins installed, I suggest you deactivating them and activating them one by another so that we can determine which plugin is causing actually issues with Email Encoder.
Alternatively, you can also check your debug.log file of WordPress if there are some issues.
The more information we can gather, the better.
Thank you already a lot.