Project Server 2010 / Sharepoint 2010 Permissions not syncing to Project Site

Question

Project Permissions not syncing to Project Site
Project Manager Group
New project is created and published project server sends permissions to Sharepoint which puts users into the following groups:
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Web Administrator (Microsoft Project Server)
Project Managers (Microsoft Project Server)
Team members (Microsoft Project Server)
Readers (Microsoft Project Server)
At this time the creator/owner, owner’s management, portfolio managers, and executives should all have Project Manager rights on the sharepoint site, and Admins will have Web Admin permissions.
Issue #1: Only the Web Admin permissions and creator/owner permissions are being added to the Sharepoint permission groups
Workaround #1: Going into the project site permissions and adding the
Project Managers (Microsoft Project Server) group manually and the sync will keep the permissions
Workaround #2: Going into the Server Settings, Manager Groups then removing or add all users to the No Permission Group, which forces an sync to all workspaces. Con: This workaround can only be down at night when users are not active since it will
block the queue for at least an hour.
Project Owner Transfer
Previously created project has owner change, once saved and published project server sends permissions to update user’s permission to
Project Managers (Microsoft Project Server) on Sharepoint project site.
Issue #2: When Project owner is changed and project is published the owner is not getting permissions to the Sharepoint project site. However, if owner is also added to the team using the Build Team Feature the sync will give the owner Project
Manager permissions on the Project Site.
Workaround #1: Going into Server Settings, Project Sites, select project and Synchronize. Once this is done, the owner will have Project Manager Permissions without being added to the team.
Users who have been added to this project in Project Server 2010, but not assigned to tasks. Users who have assignments in this project in Project Server 2010 and are contributors to the project workspace site,
meaning that they can create and edit documents, issues, and risks. Users who have published this project or who have
Save Project permission in Project Web App and are contributors to the project workspace site, meaning that they can create and edit documents, issues, and risks. Users who have
Manage SharePoint Foundation permission in Project Web App and are contributors to the project workspace site, meaning that they can create and edit documents, issues, and risks.</dir></dir>

Answer 1

By default when you create project build team add users in the task and publish the project plan then All the User which are available in the project plan including Project owner will go to below mentioned group in project site:
1. creator/owner, owner’s management, portfolio managers, and executives should all have Project Manager will get access to Project Managers (Microsoft Project Server)
2. User who are having team member access to PWA will get Team members (Microsoft Project Server) access if they are assigned to the project task.
3. User who are having team member access to PWA will get Readers (Microsoft Project Server) access if they are not assigned to the project task.
4. Only PWA Administrator will get the access to Web Administrator (Microsoft Project Server)
Sharepoint permission you have to use when you want to give permission manually to users on project site  
In the Project Site provisioning setting under Server setting if you have Check to automatically synchronize Project Web App users with Project Sites when they are created, when project managers publish projects, and when user permissions change in Project
Server.
Then all the user get access as per describe above and if you will give access manually to any of the user either in project server group or in Sharepoint group once you will publish the project next time all the manually given permission will go away.
IF you want to give permission to user manually to sharepoint group or project server group then uncheck automatically synchronize Project Web App users with Project Sites when they are created, when project managers publish projects, and when user permissions
change in Project Server.
You check PWA site setting --> Site permission then member of Sharepoint group user who will have access to sharepoint group in PWA site setting site permission will have access to all the project site sharepoint group as Project site inherit permission
from PWA root site.
Both the issue which you have described is behavior of project site.
For issue 2 when first time project owner create and publish the project and projectsite is getting created then porject owner name gets access  in the porject manager (project server group) nect time if you will change the owner and publish the project
until he will not present in the project plan will not get the permission.
If you want to give sharepoint permission to users then uncheck automatically synchronize Project Web App users with Project Sites when they are created, when project managers publish projects, and when user permissions change in Project Server and give
the permission manually. 
Project site in 2010 has some issue and not full filling customer need some time ,Ms has came up with 2013 which is having tight integration with project sites .
Project workspace security groups are equal to the SharePoint Server 2010 security groups.
Web Administrator equals Full Control
Project Managers equals Design
Team members equals Contribute
Readers equals Read
Users who have Manage
SharePoint Foundation permission in Project Web App and are contributors to the project workspace site, meaning that they can
create and edit documents, issues, and risks will get access to Web Administrator (Microsoft Project Server)
http://technet.microsoft.com/en-us/library/cc197668(v=office.14).aspx
kirtesh