Assuming you are using an HDMI connection between the TV and STB, try changing the SD Override setting; it probably is set to 480i, which causes the TV and STB to renegotiate the connection each time you change between HD and SD channels. The result is a delay in changing the channel, and for some TVs, it causes strange things to happen, like a dark screen.
To change the SD Override setting in the STB:
Menu ==> Settings ==> Video Settings ==> SD Override ==> change it to Off
Note: changing the setting to Off may make the picture on the SD channels channels slightly worse, but presumably you want to watch the HD channels most of the time, and get rid of the issue, so the change should be worth it.
If that doesn't fix it, you could go to the Pioneer website and see if there are any updates available to the TV software. If it is a new model, there probably is not, most of the HDMI negotiation are fixed in newer TVs I think.
Another alternative is to use Component (not composite) cables plus an audio cable instead of the HDMI connection. This would eliminate the HDMI negotiation that is almost certainly what is triggering what you see. Some people say the picture is worse with component connections, that is not my experience, but it may depend on the particular TV being used.