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I think that the first thing to try is to look for a 'scan to memory' option, and disable it.
If there is a memory error occurring, whereby page memory (after scanning into memory) is erasing spontaneously, then this might help.
But if there is no scan-into-memory (which is incidentally likely to be enabled if it exists on your model, since it makes all scanning / copying operations faster) on your model, then you may simply have a marginally defective scanner bar, that occasionally does not light the lamp... though I would think that would result in black pages rather than blank pages, it might work that way... or some other intermittent scanner problem. In which case there would be no workaround or settings change applicable to the problem, and you would have to decide between having the fault repair-serviced, or replacing the printer, or perhaps just replacing the scanning, faxing, and copying functions but keeping it as a printer (given that it still fully works as a printer.)
(Or disposing of it by donating it to someone that needs a printer, and to whom the copying function is either not needed, or does not need to be perfect and/or is not used a lot.)
If the printer is less than a year old, of course, the fault is covered by warranty and you should contact 1-800-OK-CANON to put in a failed-within-warranty claim on the machine, for free-of-charge repair servicing.