Ok ran into this problem for the past couple weeks.

For some reason I've been having problems starting my 93 Civic Si. Car has 235,000 miles, replaced the Main Relay back in 2007 with a new one.
Sometimes my car will start fine, other times the clock will quickly come on and everything dies. When she does restart the clock is reset and my radio too.
I took the car to Sears (where I got the battery in 2008) and they did a test on everything and nothing wrong.

I just noticed last night that when I turned my high beams on the stereo and headlights would flicker for a 1/2 second. Literally was so quick I would have thought it was just a bump in the road.

Last night I left the trickle charge on and it started fine. Got off work after 6 hours and the car wouldn't start. Turned it off, tried again nothing. Turned off and then she fired up, but clock and radio reset. Got my hair cut (took about 10 mins) and she started right up.

One more thing I noticed turning on my headlights as it has gotten cold the dash lights take 30-60 seconds to turn on, and the clock doesn't dim for the same amount.

What do you guys think it could be? Headlight switch? Ignition? Something else?

 

First check your battery connections and other grounds (make sure they are tight and clean).

 

could also be alternator

 

That was replaced in 2007. Car runs fine once she's started. Battery is full since it's showing 100% charged on my trickle charger.
The only thing I can think it could be are the wiring, the ignition (since she looks like she was broken into before I purchased her), or something funky with the headlight switch since it seems to be flaky.