Today I realized an error in my implementation of the UCI protocol. It's been there for ages and I didn't noticed because I implemented the bug in the GUI as well as in the engine so they both could communicate perfectly.
Today I plugged the engine into another GUI called Arena (available freely at http://www.playwitharena.com) and here it became obvious. The engine was not able to initialize a board position when it is not the start position.
211.172-->2: position fen 4k3/p1p3p1/1p5p/8/8/1P5P/P1P3P1/4K3 w - - 0 1
211.172-->2: go wtime 600000 btime 600000 winc 0 binc 0 movestogo 40
211.218<--2: Invalid position or FEN string !
The reason was simple. The UCI position command is followed by either the keyword 'startpos' or 'fen'. My engine just wasn't aware of the 'fen' keyword. If the GUI did not send 'startpos' the engine tried to read in the fen string and failed because 'fen' are no valid FEN characters. It responded with invalid position or FEN string.
So fixing the error was now simple, tell the engine to expect the fen keyword and start reading the actual fen input with substring 3 instead of 2. Tell the GUI to send the fen keyword before the actual FEN.
And all is well again...