I have both Cubase 6.5 32 and 64 bits versions running here without problems, so it should also be your case. One thing after the other, I would first deactivate the control room completely : it will be time to look more closely at it once your plug-ins are functional… Few things to check at first :
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What are, in the ‘Plug-ins information’ window, ‘VST plug-ins’ pane, the plug-ins missing in the list ?
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What is the path used for each plug-in actually listed ? If you use the 32 bits version of Cubase, they should be, by default, in the C:\Program Files (x86)\Steinberg\VSTPlugIns one.
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Using the ‘VST2 plug-ins paths’ button, which paths are displayed here ? Check that all paths of your plug-ins supposed to be used are listed there. Otherwise, add the missing ones.
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Do you have ‘vstpresets’ involved ? If so, you’ll have to do a rescan of all the involved locations with Mediabay.
Be also sure that the ASIO driver for your audio device is the right one in the ‘Device setup’ window, ‘VST audio system’ entry. Check also that all the ASIO in/out pairs are correctly routed in the ‘VST connections’ window, ‘Inputs’/‘Outputs’ panes.