Thank you for your response and for the bug report that you have sent from the IDE.
In general, in the 'Run specified tests' list during the deployment process we show the next tests:
- tests from your local project that are included to the deployment process; in other words, you will see those tests which you have selected for deploying to another org (if I understood properly, this works for you) or no tests from your current TWS project if you haven't selected any of local test classes;
- tests from a remote organization which this org returns to the IDE - since you can see only the tests from managed packages, this means the IDE got that only this information from your target org.
One of the possible reasons for the absent tests from the target org can be that the value of the SymbolTable for your Apex classes is empty on this organization.
To check this, please follow the next steps:
1) please open the Developer Console and Query Editor in it;
2) please paste the next query:
select Id, Name, NamespacePrefix, SymbolTable from ApexClass
3) check the 'Use Tooling API' checkbox;
4) click 'Execute' button.
Can you please let us know if all the files have data in the 'SymbolTable' column?
Also, you can create a new TWS project related to your remote organization and check if you would get the list of all the tests in the 'Run tests' wizard from this org in the IDE.
I kindly ask you also to share this information with us.
Looking forward to your response.