Every little thing matters in OCR of scans. Scans of good quality printouts of standard format sheet music or pdf's converted to tiff has to be the starting point. Figuring out the "personality" of the conversion program makes things easier as time goes on. Scanning software set to line art or black & white, darkened a bit, 300 dpi to start with (600 on difficult pieces sometimes helps), cropped to just include the bars of music gives the ocr the best chance.
You can only expect spotty results with the included "lite" version of ocr. With simple scores and the stars aligning, you can bring over the basic notes. As the scores get more complicated, it doesn't have enough resources to keep up. You will have to upgrade or pick up Sharpeye to have any sanity left after much scanning.