Thanks very much for spending time on this Max.
You were quite correct - removing the PHP Tooling plugin also removed the error windows.
Because the only thing I added to Indigo was JBoss Tools I assumed the error had to be at least related to that plugin ..... but perhaps any new server adapter would have triggered the error. I hope you didn't spend a lot of time on this.
Next time I'll try to spend more time googling the error before posting an issue.