The mircofilm reader may "time out" while you are still using your film / fiche. Just press the green button on the bottom right of the reader screen to "wake up" the machine. It should not time out while you are scanning with the Capture Perfect software, but it may time out if it takes a while to locate your information on the film.
Is your image scanning as a negative (white text on a black background)? Double check that you have selected the correct format on the left side of the microfilm / fiche reader. The green light should be showing next to your format selection.
Is your microfilm oriented the wrong way before you've even adjusted anything? Some films are already oriented as portrait or landscape. Find the dial at the top of the lens housing and turn it to change how the image is oriented on the screen. Whatever selection you decide on will translate to the scanned image.