Let me start by saying that I am not an expert on scanners, but here is my understanding about scanning fluorescent colors:
If your scanner uses CIS (Contact Image Sensor) instead of CCD (Charge-coupled Device) hardware, then the light used to illuminate whatever is being scanned comes from a combination of Red, Green, and Blue LED lights, where a scanner that uses a CCD, usually uses a fluorescent light.
It is likely that the RGB (Red, Green, Blue) LED setup just doesn't allow the dayglo/neon/fluorescent colors to "shine" (reflect) like they do under other light sources (incandescent, fluorescent, or daylight).
If your scanner will not scan the fluorescent colors, it is likely you will would need to either take photos of your work, have a professional scan made by a company that has the CCD devices or edit the image post scan using adjustments such as saturation.