Generate a PDF from VF in Apex with object context

I strongly suspect the line below in your visualforce code and it's closing tag are at the root of your problem:

<apex:pageBlockSection title="Attached Images" columns="1">

</apex:pageBlockSection>

If you look at Best Practices for Rendering PDFs you'll see that <apex:pageBlock> is listed under "Components That Are Unsafe to Use in a PDF".

I recommend you redesign your page to use other HTML (another table perhaps) instead of the <apex page block> and see if that doesn't solve your problem.

Cause: Transaction Scope

I've hit this before, and concluded this is due to how getContent is likely implemented internally. As per the Apex Documentation on transaction handling...

all changes are committed to the database only after all operations in the transaction finish executing

So the problem is until your database changes are committed, effectively not until after submitApplication method completes, no other code executions will see the changes to the record. I suspect the platform getContent method must run in a separate transaction context and thus cannot see the changes your code is making.

Solution: Chaining Execution Contexts

The solution is to invoke your logic that calls getContent and creates the attachment in a subsequent execution context (providing this one completes successfully). As it seems all async Apex features (Batch, @future) block getContent or fail silently.

We can create a new execution context via apex:actionFunction, which is invoked once the command button AJAX is complete. This example performs some DML (in my test case insert), then sets a controller member variable to pass some context to the second method invoked by the actionFunction.

public with sharing class CreateRecordAndAttachPDF {

    public Id parentId {get;set;}

    public PageReference createRecord()
    {
        Test__c test = new Test__c();
        test.A_Number__c = 42;
        insert test;            
        parentId = test.id;         
        ApexPages.addMessage(new ApexPages.Message(ApexPages.Severity.Info, 'Please wait while the attachment is made...'));            
        return null;                
    }

    public PageReference attachPDF()
    { 
        Attachment applicationpdf = new Attachment();
        applicationpdf.Body = Page.mypdf.getContentAsPdf();
        applicationpdf.ContentType = '.pdf';
        applicationpdf.Name = 'Application PDF';
        applicationpdf.Name += '.pdf';
        applicationpdf.ParentId = parentId;
        insert applicationpdf;          
        parentId = null;            
        ApexPages.addMessage(new ApexPages.Message(ApexPages.Severity.Info, 'PDF has been attached!'));   
        return null;            
    }   
}

This is the Visualforce page i used...

<apex:page controller="CreateRecordAndAttachPDF">
    <apex:form id="myform">
        <apex:pageMessages />
        <apex:commandButton 
                action="{!createRecord}"
                value="Create Record and Attach PDF" 
                rendered="{!ISNULL(ParentId)}" 
                onComplete="attachPDF();" 
                reRender="myform"/>
        <apex:actionFunction 
                name="attachPDF" 
                action="{!attachPDF}" 
                reRender="myform"/>
    </apex:form>
</apex:page>

It shows this initially...

Then when clicked this...

Then once attached this...

Hope this helps!