It seems like the error message is repeatable.
I assume site S3 is actively retrieving data from the PLC via the network. How frequently are the data retrieved and how much data? The fact that you could run without error for many hours means that there is likely no obvious problem in the ExcelLink action settings. But something happens in the communication process that throws an unknown Java exception, which causes the ExcelLink program to stop its DDE actions and therefore you need to press the Start button again to restart the process.
Can you confirm that in your program there is no possibility that the PLC could write some data out of its same serial port that was connected to the XServer? If this occurs then it can corrupt the host link communication between the XServer and the PLC and the resulting corrupted data string may cause the ExcelLink to trip.
If you are reading a large array of DM in a single action, try to break them down into two separate actions, each reading half the bank and see if it could eliminate the issue.
You can also try to upgrade to ExcelLink version 2.0 (using the upgrade link on your ExcelLink CD-ROM). The newer version may have better exception handling routine and better error reporting. However, not that version 1.03 and version 2.0 and configuration files are not compatible and you will need to re-define the actions for all the active sites.