I have not heard this issue yet, so I may ask you to run a few tests so we can identify where you are experiencing the problem. It sounds like things work fine when you install the CMS on x64, but does not work on x86.
First, make sure that you have all of the policies and your database repository are on the x86 server. If not, this is likely the issue.
It sounds like you have tried to run the framework on the x86 server. If so, manually connect to your database repository and check the policy.EvaluationErrorHistory table. You may have errors in the table indicating why the script is not able
to run against the other instances. If so, please respond with the messages.
On the x86 instance, can you please verify that you can evaluate policies through Management Studio? Navigate to a folder in the Central Management Server where you have registered the other two instances. Right click on the folder and select
"Evaluate Policies". Choose the CMS as a server source and navigate to a policy stored on the CMS. Verify that the policy evaluation completed, and make sure that you are not seeing an error in the evaluation results. If any of the policies
are returning an error, please respond with the error message.
Are you executing the framework manually through the PS console, or have you set it up as a SQL Server Agent job?