ok I have a 99 civic Si and sometimes when I crank the engine and press down on the clutch pedal the car will not shift into reverse or any gears. I recently changed my clutch master and checked if my slave was leaking no leaks.... I am thinking can it be internal ....?

 

don't think it's the clutch, it's most likely something about your shifter if you can't get it into reverse.
what do you mean it will not shift into it?
you can't get it poped in? or when it is in gear, your car wouldn't go? ect.

 

I can't pop it in when the motor is cranked and I press down on the clutch pedal it will not let me shift into any gears but when I turn the car off and shift through all the gears a couple of times it shift into gears when pressed down on the clutch

 

wow, haven't heard of this problem before...
I'd really need to look at the tranny.

 

try to pump the clutch pedal a couple times then try to go into gear and see if that works.