When you spoke to the border agents, were you firm in specifically stating the RV was not to be abandoned, sold, or otherwise dumped in Canada? This is a ticklish subject, as like all jurisdictions, all Canadian provinces want revenue from vehicles using their roads. If the RV were to be permanently set, some don't require plates/registration but some will require property taxes be paid. If the intent is to import the RV into Canada, for use in Canada, then the border agent you spoke to were correct. If the intent is to stop, mid journey, and come back to the RV to resume your travels next season, there should be no problems. This is assuming the RV is parked in storage, and not in use while sitting.
It would help if you were more specific in the locale of the storage, as some are more tenacious than others.