This might be a known issue and thee might be so many solutions to resolve this, but my issue is resolved using the method below, so I am posting this article.

Let’s say we have to upload Documents to Test1 (Source Doc Lib) and Test2 (Destination Doc Lib)Document Library simultaneously. We can achieve this task by creating SP Designer conditional workflow Refer following figure.
·         Open SharePoint Designer 2007 and then click on New > Workflow
·         On the Define your new workflow stage provide a meaningful name and select a startup type as per
your requirement.
·         Under that box you will get option to select which on which list you want to enable that workflow.
·         Click Next.
·         It will prompt you the Conditions and Actions page
·         In Condition select – Modified by specific person condition
·         Then click on specific person label and it will open option as shown in following figure
  
·         Select User who created current item option and add it to Selected Users box
·         Reason behind selecting this option is when any user uploads a document to that specific Doc Lib it will be automatically updated to destination Doc Lib
·         Then click on Actions button which will give you below option

·         Select Copy List Item option and then select copy item in Test1 (Source Doc Lib) to Test2 (Destination Doc Lib)
·         Click finish, which will finish setup of workflow on Doc Lib Test1

·         Now go to Test1 (Source Doc Lib) and upload a document.
·         In that Test1 you will see a column with the same name with which you have created a workflow, and it will give you in progress status.
·         Just go to Test2 (Destination Doc Lib) and you will get the same document listed over there.
·         And when you come back to Test1, In progress status will be over and it will give you Completed status.




Attention: One more thing I would like to specify at the end, if you have selected Manual start then you have to manually start the workflow associated on that Doc Lib.