Hi,
What scenario do you run?
1. Local Deployment (NWDS directly deploys to RTS)
2. NWDS connected to NWDI, which deploys to the RunTimeSystem (after successful assembly).
In case of 1...
Has the RunTime System (the target of your deployment) been added in Windows -> Preferences -> SAP AS Java
Else (case of 2)...
Are your custom SCs been queued (or listed as imported) for Consolidation (CMS - Transport Studio - tab Consolidation)?
Please paste the error exception from the .log file (from NWDS)
Regards