Bitstamp is a licensed and regulated exchange so you can be assured without a grain of doubt that your funds were not stolen. It might take time before you can sight the coins on your account and I believe the reason for this is that all inbound and outbound transactions on the Bitstamp system undergo a vetting process. Checks are done to ensure coins and fiat are properly accounted for and this might include passing blockchain analysis to ascertain origin and taint if any and also to check if they come from sources sanctioned by Bitstamp or the EU.

With patience and relentless querying, you will eventually see your coins. They are known to give their customers the silent treatment when something is being checked or investigated. This can be unnerving but if you have a clean conscience and if you are convinced the coins were obtained without any Mickey Mouse games, they will be credited to your account soon.