Well, the unit is switching at like 2khz at least so maybe it's just a matter of the frequency. As I said the cap is holding at 55 to 60V with this setup.

The 555 timer set up seems it would work closer to 14hz.. so thats a HUGE difference.

But there is one thing I noticed however. Despite the fact the Cap is holding at 55v the battery still only shows maybe a volt or two above charge. I'm sure the internal impedance of the battery might have something to do with this.