Ok, solved my own issue… This might be very specific, but in case anyone ever finds a similar issue:
to catch unexpected output errors I had another function:
add_action('activated_plugin','save_error');
function save_error(){
$file = "unexpected-output.txt";
$fh = fopen($file, 'w') or die("can't open file");
$error = ob_get_contents();
fclose($fh);
}
there was a typo in the fopen(), which apparently messed up things badly (still not sure why it was trying to load everything more than once – I think it has to do with the fact that the function died).
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