[SalesForce] Invalid Message Id Reference – In-Reply-To Header is Not Valid

The problem is that you are using Sets, which are unordered by nature. Since they are not reliably ordered, they may change around at any time, and if a submitted value doesn't match any of the select option values, an error will be raised. There's been some discussion about if select option values should be validated, or if it should be left to the developer to validate the values, but for now, the only workaround is to make certain that the order of the keys can't change. This error actually indicates a deeper problem, which is that if the select items were not validated, you would experience corrupted data in the controller.

This simple fix should resolve the problem:

public class selectController {

    public Map<String,List<InnerClass>> mapOfSectionAndItsClass{get;set;}
    // This is now a list
    public list<String> listOfSection{get;set;}

    public selectController(){
        mapOfSectionAndItsClass = new Map<String,List<Innerclass>>();
        listOfSection = new list<String>();

        for(Innerclass__c newContact:[SELECT Name,Low__c,Medium__c,High__c,Section__c from Innerclass__c where section__c!=NULL]){
            List<InnerClass> listOfInnerClass = new List<InnerClass>();
            if(mapOfSectionAndItsClass.containsKey(newcontact.section__c)){
                listOfInnerClass = mapOfSectionAndItsClass.get(newContact.section__c);
            }
            Innerclass newInnerclass = new Innerclass();
            newInnerclass.listOfDropdown= new List<SelectOption>();
            newInnerclass.listOfDropdown.add(new SelectOption(newContact.Low__c,newContact.Low__c));
            newInnerclass.listOfDropdown.add(new SelectOption(newContact .Medium__c,newContact.Medium__c));
            newInnerclass.listOfDropdown.add(new SelectOption(newContact.High__c,newContact.High__c)); 
            listOfInnerClass.add(newInnerclass)                       ;
            mapOfSectionandItsClass.put(newContact.section__c,listOfInnerclass);            
        }

        listOfSection.addAll(mapOfSectionandItsClass.keyset());
    }

    public pageReference check(){
        return NULL;
    }

    public class InnerClass{
        public String value{get;set;}
        public List<selectOption> listOfDropdown{get;set;}
    }

    public class Innerclass2{
        public string section{get;set;}
        public List<Innerclass> listOfInnerclasses{get;set;}
    }


}

This error normally means that an ID field referencing another object is invalid in the data.

If by "update a set of users" you mean the User SObject, that object contains self references such as "Manager" and so it is quite possible that a User early in the batch contains a reference to a User later in the batch (or a User in a later batch) and that will cause the update to fail. One way to work around this is to first load the data without the self references and then do a second pass to update the self references.

But this would only fit with your question if inadvertently during multiple upload attempts the later Users had been successfully inserted, giving the impression that the batch size was the key factor when it was not.