Thanks for the advice, I moved the timestap to the logit() subroutine and put in the test if the file exists. The code is still giving the same error.
When I run the command manually the program gives the following error:
Died at c:\FTP_Scripts\xml-ast-convert\xml-ast-convert.pl line 276.
Liner 276 is the die statement after the ftp->put() call.
The file exist test is successfull and the log file shows the correct file name and path, am I using the ftp->put() command incorrectly

#test if ast file exists
-e $astfile or die "Error: '$astfile' does not exist";

#open FTP session with remote server
$ftp=Net::FTP->new($elutionsFTP,
           Timeout=>20,
              Debug=>0,
              Passive=>1) or $err=1;
if($err){
        logit("$error_time_stamp >Unable to connect to remote FTP serv
+er $elutionsFTP\n$!");
    die;
}

#login to to remote FTP server
$ftp->login("$elutionsID", "$elutionsPWD") or $err=1;
if($err){
    logit("$error_time_stamp > Unable to login to remote FTP server $e
+lutionsFTP as $elutionsID\n$!");
    die;
}

#change directory on FTP server
$ftp->cwd($putdir) or $err=1;
if ($err) {
    logit("$error_time_stamp > Unable to change directory $putdir on $
+elutionsFTP server\n$!");
        die;
}

$ftp->binary(); # set binary mode

$ftp->put($astfile) or $err=1;
if ($err) {
    logit("$error_time_stamp > Error transferring $astfile\n$!");
        die ;
}

# Log successfull upload
logit("\n\n$error_time_stamp > Transfer successfull: FTPserver: $eluti
+onsFTP\n File: $astfile\n$!");

# End session
$ftp->quit();

exit 0;
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Log file output

Input XML file: c:\FTP_Scripts\xml-ast-convert\FTP_111100409D45C8DD_1201101600_0.xml

Output directory: c:\FTP_Scripts\xml-ast-convert
Successfully opened file: c:\FTP_Scripts\xml-ast-convert\FTP_111100409D45C8DD_1201101600_0.xml

Successfully created file: c:\FTP_Scripts\xml-ast-convert\NYPH-20101101-210000.ast

Error transferring c:\FTP_Scripts\xml-ast-convert\NYPH-20101101-210000.ast

Bad file descriptor