Please update your CS4 build to 4.0.1 or later, ideally to 4.2.1. The initial 4.0 release isn't suitable for CS4 plug-ins using the CS4 SDK. There's another thread in this forum on some of the differences:
It's normal in CS4 for the export to be passed over to Media Encoder. If your exporter is installed in the common MediaCore location described in the SDK docs, your exporter will be used by Media Encoder to do the export. In CS5, we've added a direct export route so that users can bypass Media Encoder for exporting individual clips.
I have my plugin in Plug-ins/Common/[CustomPluginFolder]/ - unless i misunderstood Media Encoder shouldn't be used authomatically in this case. I'm using SDK_Exporter sample project from CS4 SDK. exSelExport is never getting called in CS4, instead an empty Media Encoder queue window appears. The SDK_Exporter sample project from CS5 SDK works as expected with CS5 -- exSelExport does get called.
Is SDK_Exporter sample behaving correctly with CS4? What do I need to do for exSelExport to be called from CS4?
In CS4, the only export route is through Media Encoder. So you'll need to install your exporter in a place where both Premiere Pro and Media Encoder will load it. The MediaCore folder is the recommended location, which on Vista32 for CS4 will be something like:
For more info, check out Plug-in Installation on page 32 of the CS5 SDK Guide.