Warning - below is a legal description of the California law as it pertains to vehicle registrations. Ignore if you don't want to dork-out.
I did a bit of research into the issue of paying back registration on a vehicle that hadn't been registered in awhile. This comes up often with scooters, because people just don't pay the reg, and then sell them. So when you buy the bike and change the title, you have to pay all the past registrations. I read on an online forum that it was possible to get out of having to pay the back reg for a vintage vehicle, but that most people (and most DMV employees) didn't know about the law. So that got me on the road of doing some legal research into the guts of the California vehcle code...
Ok, here's the deal, as far as I can tell from the Cal Vehicle Code.
Cal. Vehicle Code § 4604 says that you have to file a non-op before the expiration of the current registration (see 4604(a)). It also says that if you file the non-op, you won't have to pay back reg when you eventually re-register it (see 4604(c)).
Significantly for us, 4604 also says that certain vehicle classes are exempt from having to file a non-op (see 4604(d)(1)-(d)(4)). Of those listed exemptions, most important for us are vehicles as described in section 5051.
Cal. Vehicle Code § 5051 provides the definition of "Collector" vehicles. Of interest for us would be the "Special Interest Vehicle". As defined by 5051(b), A "Special interest vehicle" is a vehicle of an age that is unaltered from the manufacturer's original specifications and, because of its significance, including, but not limited to, an out-of-production vehicle or a model of less than 2,000 sold in California in a model-year, is collected, preserved, restored, or maintained by a hobbyist as a leisure pursuit.
So, if you really want to get into it with the DMV, those are the California code sections you'll need. Expect to spend a little time enlightening the DMV clerk on the finer points of the law, and most likely speaking with a supervisor.
Is it worth your time to go into the DMV to contest a late fee? I guess that depends on the back reg fees you're looking at. If you're already at the DMV, and not paying by mail, I'd certainly fight the fees.