1) Shibor Swap Curve should mainly reflect the credit risk of counterparty bank. The Repo Swap Curve not only reflect the credit risk of counterparty bank, also take into account of the assets for Repo. Normally these two should be in line since the Repo assets and Chinese banks are all have same credit risk. So one explanation of difference may come from the collaterals assets.
2)When you valuate both curve, the discount curve should be same, the Chinese risk-free curve to prevent arbitrage (无套利原理)
Hope that will help you!