I actually have this and other similar symptoms happen to me all the time with the Rezound battery in the TB. I don't think it's a problem with battery life being lost - I think it's an issue within the battery's circuitry, and/or how it talks to the TB.
ANY time I charge my phone (with the Rezound battery), the phone will start charging from whatever % I'm on (obviously). It will charge up to a certain point and then level off .. and then suddenly jump from whatever that level-off point is, up to 100%. Where that level-off point is depends totally on what % I start charging at. I might level off somewhere in the 80s if I start charging in the 40s, etc. I haven't mapped out the relationship between the numbers, but I can tell you that the number doesn't truly "charge" up to 100% until I start charging up in the 80s (or so).
Same kind of thing happens with a reboot. I can reboot my phone at around 40% power and end up, after it has totally rebooted and settled back down, with only 10% left. If I reboot again I man only lose a percent or two.
Opposite happens when I reboot while the phone is plugged in. I can actually GAIN charge (numerically) if I reboot with the phone plugged in. Actually how much depends on the circumstances.
Lastly, short recharge syndrome. I can go out all day and come back in the late afternoon and be in the 30s or so. I'll plug in for a half hour and maybe charge up to (a fake number for the sake of example) say 48%. If I then unplug I'll stay at that 48% for an extremely long - definitely unrealistically long - period of time, as if the phone wasn't using any battery at all.
I chalk all these up to life with a Rezound battery in a Thunderbot. ;-) I don't think these numbers are accurate at all except perhaps in some sort of context with each other. But I'm pretty certain they're not accurate representations of the percentage of capacity of the battery. But no matter what, I still get far more out of this battery than either a 1400 or a 1700 with the Thunderbolt.