I am running PHP 5.2.14 on Apache/2.2.16 (Win32) and I have a script to run a shell command, which when tested in the command prompt works well but in browser mode (html), it doesn't.

Scripts:

mybatfile.bat

REM ...
REM process some folder details
REM code which does not work in browser mode but works in cmd mode
C:/somfolder/bin/mysqldump -u abc -pabcdef --result-file="C:/Apache22/somfolder/DBbackup/DBbackup.%DATE:~10,4%%DATE:~4,2%%DATE:~7,2%.sql" --dump-date  --log-error="C:/Apache22/somfolder/DBbackup/DBbackup.%DATE:~10,4%%DATE:~4,2%%DATE:~7,2%.log" dbname > dboutputresult.txt

REM process result of savedfile

calltobatfile.php

//process some folder information
$file = file_get_contents($folderroot."/exec/mybatfile.bat");
//var_dump($file);
    $strarr = explode("\n", $file);
    foreach($strarr as $line){
      if(strlen($line)>1){
        var_dump("line: ".$line."\n"); 
        $output = shell_exec($line);
        print_r($output);
     }
   }

//process result of savedfile additional information

What can I try next?

Check the permissions to run it as a server. You can run this as owner, but there can be no possibilities to run it as other user - in your example as apache.