Possible bug report with the latest Beta version of Orbiter...
IMS was not designed to work with orbiter Beta, and never will be... we're working on a follow-up for that. Currently it is not known whether the thing will work with any kind of stability in the Beta. I'm still glad for any Beta-specific bug reports though, since they might be early warning signs of trouble we will run into with the new version.
I have four dark boxes in my view
Those would be the MFDs, which should be transparent, but aren't, because the Beta renders switched off MFDs. The problem was known for quite a while.
I can't seem to get the cockpit to do anything.
This, however, is most probably because either the vessel still has its transport seal, or the command module is unpowered. In both cases, the flight panel is not available. press ctrl-down to get to the engineering panel.