It seems that the Apple firmware is more tolerant to voltage swings than Rockbox is, or is capable of dynamic reading and estimation. Rockbox makes a number of assumptions in this regard, which while badly calibrated for this specific device in terms of estimated time remaining (which doesn't affect actual runtime or percentile display), generally work out OK.
There's a couple of things you could try, but you might end up having to try both of them. One is delaying the first battery reading to ensure that the battery has settled after initial disk access and CPU boost draw. The other is outright lying.
Both are
explained in this short thread, I even give a very specific example there for delaying reading specific to the iPod Classic. The outright lying will need trial and error depending on exactly how bad your battery is.
[Saint]