I've tried to replicate this using the following code:
$fileType = 'Excel2007';
$fileName = 'testBinderTime.xlsx';
$objReader = PHPExcel_IOFactory::createReader($fileType);
$objPHPExcel = $objReader->load($fileName);
$sheet = $objPHPExcel->getActiveSheet();
PHPExcel_Cell::setValueBinder( new PHPExcel_Cell_AdvancedValueBinder() );
$timeNow = date('H:i:s');
$objPHPExcel->getActiveSheet()->setCellValue('A' . ($sheet->getHighestRow() + 1), $timeNow);
$objWriter = PHPExcel_IOFactory::createWriter($objPHPExcel, $fileType);
but it is working exactly as I'd expect it to work.
I've tried this with both Excel5 and Excel2007, without seeing any of the previous values changing format in any way.
The only thing that I can think of is that you're reading the workbook with setReadDataOnly(true), which is telling PHPExcel not to read any format masking (which includes date masking).
Is it possible for you to create a code snippet that demonstrates this problem?