Interesting.
Seems like the local database is not loaded properly for some reason.
I guess the problem resides in the main process.
Could you please run the app from terminal by the following command?
> /Applications/Inkdrop.app/Contents/MacOS/Inkdrop
And let me know error logs.
Also please try reloading the browser window by selecting menu Developer -> Reload.
If it were a race condition issue, the app should load properly.