I was watching my energy recharge timer and it went 3 2 1 0 1 THEN reset.... is this extra second normal?

Mines tends to stick at 0 for a couple of seconds, but then skip a few into the next one. If it's only 1 second just add another power conduit.

I can't it caps out at 4+2 Fathers

the problem usually stops when you get to positronic relays. or wave conduits. one of the two. anyway, if the problem persists try clearing the cache (that fixes 99% of bugs with this game) and if it still persists, then try getting a plasma hub. you can fit 3 of those on your ship.

i've seen it do it even with wormhole relays...

what's happening is somehow the client side gets out of sync... when the timer hits 0, it queries the server for a resync...